Rwanda Baseline Demographic and Soil Summary and Analysis

Objective: Summary of the demographics and soil characteristics of the Rwanda long term soil health study.

Study methodology

Add in details and links on study methodology here.

library(knitr)
library(ggplot2)
library(stringr)
suppressMessages(library(dplyr))
library(sp)
suppressMessages(library(rgdal))
suppressMessages(library(dismo))
suppressMessages(library(stargazer))
library(leaflet)
library(XML)
suppressMessages(library(maptools))
library(automap)
suppressMessages(library(RStata))
suppressMessages(library(fields))
library(gstat)
library(htmltools)
suppressMessages(library(Matching))
options("RStata.StataVersion" = 12)
options("RStata.StataPath" = "/Applications/Stata/StataSE.app/Contents/MacOS/stata-se")
#chooseStataBin("/Applications/Stata/StataSE.app/Contents/MacOS/stata-se")

wd <- "/Users/mlowes/drive/soil health study/data/rw baseline"
dd <- paste(wd, "data", sep = "/")
od <- paste(wd, "output", sep="/")
md <- paste(wd, "maps", sep="/")
drive <- "~/drive/r_help/4_output/statistical_test_outputs"

#load data:
# This data is being drawn from the Soil lab repository. It has the baseline data with it
# d <- read.csv(paste(dd, "Rwanda_shs_commcare_soil_data_final.csv", sep="/"),  stringsAsFactors=FALSE)

Combine survey and soil data

Replicate Alex’s and Emmanuel’s merge process using “Identifiers with SSN_final” provided by Emmanuel. I use the RStata package found here

# I'm replicating Alex's do file here.
stata("merge_shs.do")

## . * merge raw commcare data with soil database
## . 
## . * date: 11 july 2016
## . 
## . clear all
## . set more off
## . 
## . * set directory
## . global wd "/Users/mlowes/drive/soil health study/data/rw baseline"
## . global dd "/Users/mlowes/drive/soil health study/data/rw baseline/data"
## . global troubleshoot "/Users/mlowes/drive/soil health study/data/rw baseline/t
## > roubleshoot"
## . 
## . * insheet data
## . insheet using "$dd/raw_rwanda_commcare_shs.csv", clear
## (94 vars, 2491 obs)
## . 
## . * clean sample_id variable
## . replace sample_id = "" if sample_id == "---"
## (10 real changes made)
## . replace sample_id = "-99" if sample_id == "99"
## (19 real changes made)
## . 
## . destring sample_id, replace
## sample_id has all characters numeric; replaced as int
## (10 missing values generated)
## . 
## . * manipulate current "sample_id" to become a proper alpha-numeric unique iden
## > tifier
## . * this simply involves adding "C" to each numeric code that belongs to a cont
## > rol farmer
## . 
## . * variables of interest:
## .       * d_client
## .       * sample_id
## . 
## . ren demographic_infod_client d_client
## . replace d_client = "" if d_client == "---"
## (10 real changes made)
## . destring d_client, replace
## d_client has all characters numeric; replaced as byte
## (10 missing values generated)
## . 
## . tostring sample_id, gen(sample_id_string)
## sample_id_string generated as str4
## . 
## . replace sample_id_string = sample_id_string + "C" if d_client == 0
## sample_id_string was str4 now str5
## (1236 real changes made)
## . drop sample_id 
## . ren sample_id_string sample_id
## . 
## . ***** !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ***
## > ***
## . * quantify and note cases where sample_id appears more than twice
## .      * 39 codes appear 2x
## .      * 1 code appears 3x
## .      * 1 code appears 4x
## .      * 1 code appears 10x
## .      * 1 code appears 19x
## . 
## . duplicates report sample_id
## 
## Duplicates in terms of sample_id
## 
## --------------------------------------
##    copies | observations       surplus
## ----------+---------------------------
##         1 |         2377             0
##         2 |           78            39
##         3 |            3             2
##         4 |            4             3
##        10 |           10             9
##        19 |           19            18
## --------------------------------------
## . duplicates tag sample_id, gen(n_duplicate_id)
## 
## Duplicates in terms of sample_id
## . gen d_id_problem = 1 if n_duplicate_id != 0
## (2377 missing values generated)
## . replace d_id_problem = 0 if missing(d_id_problem)
## (2377 real changes made)
## . 
## . ** need to investigate 5% of observations (114 samples), i.e. d_id_problem = 
## > 1**
## . ***** !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ***
## > ***
## . 
## . * outsheet problematic observations and examine 1-by-1
## . sort sample_id
## . outsheet demographicnom_enqueteur district demographic_infocellule_selected d
## > emographic_infoumudugudu d_client demographic_infonom_cultivateur sample_id d
## > emographic_infosex demographic_infoage_cultivateur demographic_infon_telephon
## > e_cult d_id_problem using "$dd/shs_to_check.csv" if d_id_problem == 1, replac
## > e comma
## . 
## . **************** post-investigation correction of incorrect ids *************
## > ***
## . 
## . ren demographic_infonom_cultivateur farmer_name
## . ren demographic_infocellule_selected selected_cell
## . ren demographicnom_enqueteur enumerator_name
## . 
## . * drop test/accidentally double-entered observations
## . drop if infoformid == "f138897f-6e80-4b0a-9db3-ab2134cd9e51"
## (1 observation deleted)
## . drop if farmer_name == "Mugisha"
## (1 observation deleted)
## . drop if farmer_name == "Muhunde yoramu"
## (1 observation deleted)
## . drop if farmer_name == "Test"
## (1 observation deleted)
## . drop if farmer_name == "Billy"
## (1 observation deleted)
## . drop if farmer_name == "Gakuba michel"
## (2 observations deleted)
## . drop if farmer_name == "Renata"
## (1 observation deleted)
## . drop if farmer_name == "Bub"
## (1 observation deleted)
## . drop if farmer_name == "M"
## (1 observation deleted)
## . drop if farmer_name == "Anita"
## (1 observation deleted)
## . drop if farmer_name == "Jean"
## (1 observation deleted)
## . drop if farmer_name == "Nyirazaninka lea"
## (1 observation deleted)
## . drop if farmer_name == "Mugiraneza Pacifiue"
## (1 observation deleted)
## . drop if farmer_name == "Nsengiyaremye Innocent"
## (1 observation deleted)
## . 
## . * correct incorrectly recorded ids
## . replace sample_id = "880C" if farmer_name == "Nyiransanzineza Marie Rose"
## (1 real change made)
## . replace sample_id = "811C" if farmer_name == "Ngirabatware  Daniel"
## (1 real change made)
## . replace sample_id = "646C" if farmer_name == "Nyirasabwa anonciata"
## (1 real change made)
## . replace sample_id = "624C" if farmer_name == "Nyirinkindi j Bosco"
## (1 real change made)
## . replace sample_id = "560C" if farmer_name == "Mubirigi Bertin"
## (1 real change made)
## . replace d_client = 0 if farmer_name == "Mubirigi Bertin"
## (1 real change made)
## . replace sample_id = "375C" if farmer_name == "Hitimana ezecquiere"
## (1 real change made)
## . replace sample_id = "322C" if farmer_name == "Nyirantabire arrivera"
## (1 real change made)
## . replace sample_id = "2566C" if farmer_name == "MUSABYIMANA Colletta"
## (1 real change made)
## . replace sample_id = "2399C" if farmer_name == "Nyirabajyambere anastisia"
## (1 real change made)
## . replace d_client = 0 if farmer_name == "Nyirabajyambere anastisia"
## (1 real change made)
## . replace sample_id = "2280C" if farmer_name == "Zihabake Simon"
## (1 real change made)
## . replace sample_id = "2202C" if farmer_name == "mugiraneza pacifique"
## (1 real change made)
## . replace sample_id = "1780C" if farmer_name == "Hakuzimana Theophile"
## (1 real change made)
## . replace sample_id = "1757C" if farmer_name == "Bavugirije Feleciane"
## (1 real change made)
## . replace sample_id = "1626C" if farmer_name == "Nyabivumu"
## (1 real change made)
## . replace sample_id = "1575C" if farmer_name == "BAHIMBANDE Beriyana."
## (1 real change made)
## . replace d_client = 0 if farmer_name == "BAHIMBANDE Beriyana."
## (1 real change made)
## . replace sample_id = "1103C" if farmer_name == "Barirwanda Elyse"
## (1 real change made)
## . replace sample_id = "1037C" if farmer_name == "Mukashema Faraziya"
## (1 real change made)
## . replace d_client = 0 if farmer_name == "Mukashema Faraziya" 
## (1 real change made)
## . replace sample_id = "3069" if farmer_name == "Ndababonye Silas"
## (1 real change made)
## . replace sample_id = "2611" if farmer_name == "Sebazungu modeste"
## (1 real change made)
## . replace d_client = 1 if farmer_name == "Sebazungu modeste"
## (1 real change made)
## . replace sample_id = "2415" if farmer_name == "Nkaka joseph"
## (1 real change made)
## . replace sample_id = "2412" if farmer_name == "Ndagijimana alexis"
## (1 real change made)
## . replace sample_id = "2410" if farmer_name == "Sebuhoro elie"
## (1 real change made)
## . replace sample_id = "2406" if farmer_name == "Mugisha ruth"
## (1 real change made)
## . replace sample_id = "2405" if farmer_name == "Mboneza hasan"
## (1 real change made)
## . replace sample_id = "2404" if farmer_name == "Ntibitonderwa veriane"
## (1 real change made)
## . replace sample_id = "2399" if farmer_name == "Nyiraburakeye feresita"
## (1 real change made)
## . replace sample_id = "2395" if farmer_name == "Uwimana danier"
## (1 real change made)
## . replace sample_id = "2394" if farmer_name == "Bizinde silas"
## (1 real change made)
## . replace sample_id = "2390" if farmer_name == "Nyirahabimvana keresesiya"
## (1 real change made)
## . replace sample_id = "2388" if farmer_name == "Nyirasekerabanzi tharcilla"
## (1 real change made)
## . replace sample_id = "2386" if farmer_name == "Ndererimana emmanuel"
## (1 real change made)
## . replace sample_id = "2291" if farmer_name == "Ndacyayisenga Feresiyani"
## (1 real change made)
## . replace sample_id = "2184" if farmer_name == "Muhawenimana Beretirida"
## (1 real change made)
## . replace sample_id = "2145" if farmer_name == "Fapfakwita celestine"
## (1 real change made)
## . replace sample_id = "2141" if farmer_name == "Nsangiranabo krizoroji"
## (1 real change made)
## . replace sample_id = "2140" if farmer_name == "Nsabyumuremyi anakereti"
## (1 real change made)
## . replace sample_id = "2136" if farmer_name == "Nyirantibitonderwa savoroniya"
## (1 real change made)
## . replace sample_id = "2131" if farmer_name == "Hagenimana Ewufroni"
## (1 real change made)
## . replace sample_id = "2066" if farmer_name == "Hitayezu vicent"
## (1 real change made)
## . replace d_client = 1 if farmer_name == "Hitayezu vicent"
## (1 real change made)
## . replace sample_id = "2044" if farmer_name == "Niyodushima janette"
## (1 real change made)
## . replace d_client = 1 if farmer_name == "Niyodushima janette"
## (1 real change made)
## . replace sample_id = "2024" if farmer_name == "Mukabatsinda veren A"
## (1 real change made)
## . replace sample_id = "2020" if farmer_name == "Sibomana innocent"
## (1 real change made)
## . replace sample_id = "2009" if farmer_name == "Nsabimana inyasi"
## (1 real change made)
## . replace sample_id = "2002" if farmer_name == "Mateso elizabet"
## (1 real change made)
## . replace sample_id = "1889" if farmer_name == "Niyonsaba Daniel"
## (1 real change made)
## . replace sample_id = "1864" if farmer_name == "Mukankubana Souzanne"
## (1 real change made)
## . replace sample_id = "1780" if farmer_name == "Nyirantihabose Annonciatha"
## (1 real change made)
## . replace sample_id = "1771" if farmer_name == "Bizimungu Damascne"
## (1 real change made)
## . replace sample_id = "1675" if farmer_name == "Bikorimana Isaac"
## (1 real change made)
## . replace sample_id = "1103" if farmer_name == "Munyabarata japhette"
## (1 real change made)
## . replace sample_id = "954" if farmer_name == "Hahirwabake silver"
## (1 real change made)
## . replace sample_id = "541" if farmer_name == "Rugemintwaza Vianney"
## (1 real change made)
## . replace sample_id = "454" if farmer_name == "Niyonizeye fororida"
## (1 real change made)
## . replace sample_id = "407" if farmer_name == "Munyaneza jean pierre"
## (1 real change made)
## . replace sample_id = "375" if farmer_name == "Munyarubuga nanias"
## (1 real change made)
## . replace sample_id = "322" if farmer_name == "Gacandaga zackarie"
## (1 real change made)
## . replace sample_id = "262" if farmer_name == "MUHIRWA J Damascene"
## (1 real change made)
## . replace sample_id = "32" if farmer_name == "Nsanzemuhire"
## (1 real change made)
## . 
## . *** re-run duplicates test
## . drop d_id_problem
## . drop n_duplicate_id
## . 
## . duplicates report sample_id
## 
## Duplicates in terms of sample_id
## 
## --------------------------------------
##    copies | observations       surplus
## ----------+---------------------------
##         1 |         2464             0
##         2 |           12             6
## --------------------------------------
## . duplicates tag sample_id, gen(n_duplicate_id)
## 
## Duplicates in terms of sample_id
## . gen d_id_problem = 1 if n_duplicate_id != 0
## (2464 missing values generated)
## . replace d_id_problem = 0 if missing(d_id_problem)
## (2464 real changes made)
## . 
## . * second try: outsheet problematic observations and examine 1-by-1
## . sort sample_id
## . outsheet using "$dd/shs_to_check_2.csv" if d_id_problem == 1, replace comma
## . 
## . * second try: correct incorrect ids
## . 
## . replace sample_id = "2202" if farmer_name == "Mukamurara scholastique"
## (1 real change made)
## . replace d_client = 1 if farmer_name == "Mukamurara scholastique"
## (1 real change made)
## . replace sample_id = "2195" if farmer_name == "Ndacyayisenga Feresiyani"
## (1 real change made)
## . replace sample_id = "824" if farmer_name == "Ngirabatware  Daniel"
## (1 real change made)
## . 
## . replace sample_id = "" if rownumber == 238
## (1 real change made)
## . replace sample_id = "" if rownumber == 848
## (1 real change made)
## . replace sample_id = "" if rownumber == 1257
## (1 real change made)
## . replace sample_id = "" if rownumber == 1732
## (1 real change made)
## . 
## . *** re-run duplicates test
## . drop d_id_problem
## . drop n_duplicate_id
## . 
## . duplicates report sample_id
## 
## Duplicates in terms of sample_id
## 
## --------------------------------------
##    copies | observations       surplus
## ----------+---------------------------
##         1 |         2472             0
##         4 |            4             3
## --------------------------------------
## . duplicates tag sample_id, gen(n_duplicate_id)
## 
## Duplicates in terms of sample_id
## . gen d_id_problem = 1 if n_duplicate_id != 0
## (2472 missing values generated)
## . replace d_id_problem = 0 if missing(d_id_problem)
## (2472 real changes made)
## . 
## . * third try: outsheet problematic observations
## . sort sample_id
## . outsheet using "$dd/shs_to_check_3.csv" if d_id_problem == 1, replace comma
## . 
## . *** 4 sets of duplicates remain (2 observations)
## . drop if d_id_problem == 1
## (4 observations deleted)
## . save "$dd/rwanda_commcare_shs_clean.dta", replace
## file /Users/mlowes/drive/soil health study/data/rw baseline/data/rwanda_commcar
## > e_shs_clean.dta saved
## . outsheet using "$dd/rwanda_commcare_shs_clean.csv", comma replace
## . 
## . * merge datasets
## . insheet using "$dd/mne_rwanda_database_shs.csv", clear
## (28 vars, 2483 obs)
## . 
## . save "$dd/mne_rwanda_database_shs.dta", replace
## file /Users/mlowes/drive/soil health study/data/rw baseline/data/mne_rwanda_dat
## > abase_shs.dta saved
## . 
## . use "$dd/rwanda_commcare_shs_clean.dta", clear
## . 
## . merge 1:1 sample_id using "$dd/mne_rwanda_database_shs.dta"
## 
##     Result                           # of obs.
##     -----------------------------------------
##     not matched                            93
##         from master                        41  (_merge==1)
##         from using                         52  (_merge==2)
## 
##     matched                             2,431  (_merge==3)
##     -----------------------------------------
## . 
## .    * 93 observations unmatched... :(
## . 
## . * investigate unmatched observations
## . sort sample_id
## . outsheet using "$troubleshoot/unmatched_commcare.csv" if _merge == 1, comma r
## > eplace
## . outsheet using "$troubleshoot/unmatched_inventory.csv" if _merge == 2, comma 
## > replace
## . 
## . * make first round of corrections in master data
## . use "$dd/rwanda_commcare_shs_clean.dta", clear
## . 
## . replace sample_id = "2711C" if farmer_name == "Kamuhanda Elie"
## (1 real change made)
## . replace sample_id = "260C" if farmer_name == "HATEGEKIMANA Mathias"
## (1 real change made)
## . replace sample_id = "245" if farmer_name == "Kayiranga Michel"
## (1 real change made)
## . replace sample_id = "1543" if farmer_name == "Ndagijimana Eliezel"
## (1 real change made)
## . replace sample_id = "1543C" if farmer_name == "Mukantanganzwa odeta"
## (1 real change made)
## . replace sample_id = "1632" if farmer_name == "Nyiranziguye Cecile"
## (1 real change made)
## . replace sample_id = "2782" if farmer_name == "Mukamungu leocadie"
## (1 real change made)
## . replace sample_id = "421C" if farmer_name == "Niyonizeye Francine"
## (1 real change made)
## . replace sample_id = "828C" if farmer_name == "Mukamazimpaka Terese"
## (1 real change made)
## . replace sample_id = "364" if farmer_name == "Mukamuyango verina"
## (1 real change made)
## . replace sample_id = "364C" if farmer_name == "Mujawimana jeanne"
## (1 real change made)
## . replace sample_id = "368" if farmer_name == "Nyiramanzi jean damascene"
## (1 real change made)
## . replace sample_id = "368C" if farmer_name == "Karwiyegura rachel"
## (1 real change made)
## . replace sample_id = "391" if farmer_name == "Mugemane augistin"
## (1 real change made)
## . replace sample_id = "391C" if farmer_name == "Ngirishuti sumayire"
## (1 real change made)
## . replace sample_id = "395" if farmer_name == "Niyomugabo amiel"
## (1 real change made)
## . replace sample_id = "395C" if farmer_name == "Ntawiniga augustin"
## (1 real change made)
## . replace sample_id = "396" if farmer_name == "Mpayimana philippe"
## (1 real change made)
## . replace sample_id = "329" if farmer_name == "Mucyezangango emmanuel"
## (1 real change made)
## . replace sample_id = "411" if farmer_name == "Nsabimana mathias"
## (1 real change made)
## . replace sample_id = "411C" if farmer_name == "Singirankabo"
## (1 real change made)
## . replace sample_id = "414" if farmer_name == "Rutaharama eldephonse"
## (1 real change made)
## . replace sample_id = "329C" if farmer_name == "Mukamana josephine"
## (1 real change made)
## . replace sample_id = "657" if farmer_name == "Nyandwi vincent"
## (1 real change made)
## . replace sample_id = "569C" if farmer_name == "Uwimana Bercilla"
## (1 real change made)
## . replace sample_id = "2051C" if farmer_name == "Ntambabazi Anastase"
## (1 real change made)
## . replace sample_id = "2249" if farmer_name == "Uwineza valentine"
## (1 real change made)
## . replace sample_id = "2360C" if farmer_name == "Bamporineza j deDieu"
## (1 real change made)
## . replace sample_id = "2001" if farmer_name == "Nyiramakuba thanene"
## (1 real change made)
## . replace sample_id = "2897C" if farmer_name == "Mukagatanazi Marianne"
## (1 real change made)
## . replace sample_id = "2965C" if farmer_name == "Twizeyimana Theoneste"
## (1 real change made)
## . 
## . drop if farmer_name == "Yjk"
## (1 observation deleted)
## . drop if farmer_name == "Uwambajimana Agnes"
## (1 observation deleted)
## . drop if farmer_name == "Tr"
## (1 observation deleted)
## . 
## . replace sample_id = "2415C" if farmer_name == "Nyiramahirwe Frolance"
## (1 real change made)
## . replace sample_id = "851" if farmer_name == "Bigirimana  Amon"
## (1 real change made)
## . 
## . 
## . * duplicates check
## . drop d_id_problem
## . drop n_duplicate_id
## . 
## . duplicates report sample_id
## 
## Duplicates in terms of sample_id
## 
## --------------------------------------
##    copies | observations       surplus
## ----------+---------------------------
##         1 |         2469             0
## --------------------------------------
## . duplicates tag sample_id, gen(n_duplicate_id)
## 
## Duplicates in terms of sample_id
## . gen d_id_problem = 1 if n_duplicate_id != 0
## (2469 missing values generated)
## . replace d_id_problem = 0 if missing(d_id_problem)
## (2469 real changes made)
## . 
## . * second try: merge
## . merge 1:1 sample_id using "$dd/mne_rwanda_database_shs.dta"
## 
##     Result                           # of obs.
##     -----------------------------------------
##     not matched                            24
##         from master                         5  (_merge==1)
##         from using                         19  (_merge==2)
## 
##     matched                             2,464  (_merge==3)
##     -----------------------------------------
## . 
## . * deal with 30 unmatched cases
## . sort sample_id
## . outsheet using "$troubleshoot/unmatched_commcare_2.csv" if _merge == 1, comma
## >  replace
## . outsheet using "$troubleshoot/unmatched_inventory_2.csv" if _merge == 2, comm
## > a replace
## . 
## . * 5 submitted surveys with no corresponding sample
## . *drop if _merge == 1
## . 
## . * 19 samples with no corresponding survey
## . *drop if _merge == 2
## . 
## . * outsheet merged database
## . outsheet using "$dd/rwanda_shs_baseline_data.csv", comma replace
## . * THIS IS THE CLEAN VERSION! ONLY USE THIS! DON'T USE OTHER THINGS!
## .

Import the results of Alex’s do file.

d <- read.csv(paste(dd, "rwanda_shs_baseline_data.csv", sep = "/"), stringsAsFactors = F)
Identifiers <- read.csv(paste(dd, "Identifiers with SSN_final.csv", sep = "/"), stringsAsFactors = F)

wetChem <- read.csv(paste("/Users/mlowes/drive/JuPyteR/robert.on@oneacrefund.org/Rwanda Acidity", "Original chem_rwanda_shs.csv", sep = "/"))


d <- left_join(d, Identifiers, by="sample_id")

# now import the soil results and merge with survey data
soilRF <- read.csv(paste(dd, "rwshs_rfresults.csv", sep = "/"), stringsAsFactors = F)
names(soilRF)[names(soilRF)=="X"] <- "SSN"

d <- left_join(d, soilRF, by="SSN")

Cleaning baseline variables

Now let’s start cleaning the demographic variables

# take out weird CommCare stuff
d[d=="---"] <- NA

names(d) <- gsub("text_final_questions", "", names(d))
names(d) <- gsub("intro_champ_echantillon", "", names(d))
names(d) <- gsub("demographic_info", "", names(d))
names(d) <- gsub("other_inputs_", "", names(d))
names(d) <- gsub("crop1_15b_inputs", "", names(d))
names(d) <- gsub("crop2_15b_inputs", "", names(d))
names(d) <- gsub("^15b", "", names(d))
names(d) <- gsub("historical_intro", "", names(d))

names(d)[names(d)=="field_dim"] <- "field_dim1"
names(d)[names(d)=="v51"] <- "field_dim2"

Take care of demographic data formatting issues

# deal with names and drop unnecessary variables
d <- d %>% 
    dplyr::select(-c(rownumber, infoformid, introductiond_accept, photo,
        infocompleted_time, 
        enumerator_name, contains("phone"), farmer_name, farmersurname, farmername,
        d_respondent, additionalsamplepackedandsenttol, additionalsamplerequestedfromlab,
        datedryingcompleteifnecessary, driedindistrictifnecessary, senttohqyo,
        collectedindistrictyo, excessstoredathq_, receivedathq_,dateofinitialdryingifnecessary,
        samplecollectedinfieldyo, field_des, samplewetordry)) %>%
    rename(
    female = sex,
    age = age_cultivateur,
    own = d_own,
    client = d_client) %>%
    mutate(
    female= ifelse(female=="gore", 1,0),
    field.size = field_dim1*field_dim2
    )

d$total.seasons <- apply(d[, grep("d_season_list", names(d))], 1, function(x) {
    sum(x, na.rm=T)})

Check out client variable - why are there missing values?

table(d$client, useNA = 'ifany')

## 
##    0    1 <NA> 
## 1233 1236   19

d[is.na(d$client), c("sample_id")]

##  [1] "1189C" "1207C" "1295"  "1295C" "1298C" "1300"  "1300C" "1366C"
##  [9] "1476C" "1485C" "1554"  "1573"  "1614"  "2042"  "2371C" "2373" 
## [17] "2375"  "2382"  "2442"

# replace client based on whether there is a C in the client variable.
d$client.check <- ifelse(grepl("C", d$sample_id)==T, 0, 1)
table(d$client, d$client.check)

##    
##        0    1
##   0 1233    0
##   1    1 1235

It looks like most farmers were recorded correctly except for one farmer who was coded as Tubura farmer but their sample_id indicate their a control. Let’s take a look:

d[d$client==1 & d$client.check==0 & !is.na(d$d_gps), c("sample_id", "tuburacontroltc")]

##     sample_id tuburacontroltc
## 990     2202C         Control

# they should be a control
d[d$client==1 & d$client.check==0 & !is.na(d$d_gps), "client"] <- 0

# remove farmers for which we have soil data but no survey data (using)
d <- d[-which(grepl("using", d$X_merge)),]
table(d$client, d$client.check, useNA = 'ifany')

##    
##        0    1
##   0 1234    0
##   1    0 1235

# update client to equal client check
d$client <- d$client.check

Fix some more variable names:

names(d)[names(d)=="field_kg_fert1_1"] <- "field_kg_fert1_15b"
names(d)[names(d)=="field_kg_fert2_1"] <- "field_kg_fert2_15b"
names(d)[names(d)=="field_kg_compost"] <- "field_kg_compost_15b"

Recode variables to numeric:

# recode to numeric
varlist <- c("client", "own", "crop1_15b_seedkg", "crop1_15b_yield", "crop1_15b_yield_",
    "crop2_15b_seedkg", "crop2_15b_yield", "crop2_15b_yield_", "field_kg_fert1_15b",
    "field_kg_fert2_15b", "field_kg_compost_15b", "d_lime_15b", "kg_lime_15b")

# check that there aren't values hidden in the character variables
#apply(d[,varlist], 2, function(x){table(x, useNA='ifany')})

# recode characters to numerics
d[, varlist] <- sapply(d[,varlist], as.numeric)

# divide out GPS coordinates
# http://rfunction.com/archives/1499

# replace the blank gps_pic_guide with info
d <- cbind(d, str_split_fixed(d$gps_pic_guid, " ", n=4))
names(d)[107:110] <- c("lat", "lon", "alt", "precision")
d[,c("lat", "lon", "alt", "precision")] <- sapply(d[,c("lat", "lon", "alt", "precision")],
                                                  function(x){as.numeric(as.character(x))})

Cleaning soil data

Cleaning of soil data: Come back, check and clean the soil data before outputting to clean data set. Plot each of the soil variables to look for unrealistic values.

dim(d[is.na(d$m3.Ca),])

## [1]  26 110

d <- d[-which(is.na(d$m3.Ca)),]
       
summary(d[,c("m3.Ca", "m3.Mg", "pH", "Total.N", "Total.C")])

##      m3.Ca            m3.Mg               pH           Total.N       
##  Min.   : 220.5   Min.   :  38.26   Min.   :4.547   Min.   :0.05523  
##  1st Qu.: 443.0   1st Qu.: 114.16   1st Qu.:5.021   1st Qu.:0.13596  
##  Median : 720.2   Median : 184.98   Median :5.539   Median :0.15552  
##  Mean   : 876.4   Mean   : 207.82   Mean   :5.544   Mean   :0.15717  
##  3rd Qu.:1157.9   3rd Qu.: 270.26   3rd Qu.:6.009   3rd Qu.:0.17886  
##  Max.   :3669.2   Max.   :1008.93   Max.   :7.211   Max.   :0.24701  
##     Total.C      
##  Min.   :0.8988  
##  1st Qu.:1.7227  
##  Median :2.1118  
##  Mean   :2.1096  
##  3rd Qu.:2.3657  
##  Max.   :4.1620

Let’s check out the rows for which we don’t have soil data and drop them as they won’t contribute to the full picture.

Graphs of RW baseline soil variables

soilVars <- c("m3.Ca", "m3.Mg", "pH", "Total.N", "Total.C")
for(i in 1:length(soilVars)){
print(
  ggplot(data=d, aes(x=as.factor(client), y=d[,soilVars[i]])) + 
    geom_boxplot() +
    labs(x="Tubura Farmer", y=soilVars[i], title = paste("RW baseline soil - ", soilVars[i], sep = ""))
  )  
}

Check out soil relationships

There are biologically predictable relationships between soil chemical characteristics. For instance, we expect Ca and Mg to move in the same direction and be positively correlated with pH. If we had Aluminum as an outcome, we’d expect pH to be negatively correlated with soluable aluminum. Let’s look quickly to confirm if those relationships are present:

ggplot(d, aes(x=m3.Ca, y=m3.Mg)) + geom_point() +
    stat_smooth(method="loess") +
    labs(x = "Calcium (m3)", y= "Magnesium (m3)", title="Calcium and Magnesium relationship")

ggplot(d, aes(x=pH, y=m3.Ca)) + geom_point() +
  stat_smooth(method="loess") +
  labs(x = "pH", y="Calcium (m3)", title = "pH and Calcium relationship")

ggplot(d, aes(x=pH, y=m3.Mg)) + geom_point() +
  stat_smooth(method="loess") +
  labs(x = "pH", y="Magnesium (m3)", title = "pH and Magnesium relationship")

ggplot(d, aes(x=Total.C, y=Total.N)) + geom_point() + 
  stat_smooth(method="loess") +
  labs(x = "Total Carbon", y="Total Nitrogen", title = "Carbon and Nitrogen relationship")

The soil characteristics are moving in the manner that is consistent with our understanding of soil chemical processes.

Save clean demographic and soil data to external file

write.csv(d, file=paste(dd, "shs rw baseline.csv", sep = "/"))
save(d, file=paste(dd, "shs rw baseline.Rdata", sep = "/"))

Map of baseline observations

Produce a simple map of where our observations are

See here for more on using markerClusterOptions in leaflet.

In the map below, the larger green circles are Tubura farmers and the smaller blue circles are control farmers.

e <- d[!is.na(d$lon),]
ss <- SpatialPointsDataFrame(coords = e[, c("lon", "lat")], data=e)

pal <- colorNumeric(c("navy", "green"), domain=unique(ss$client))
map <- leaflet() %>% addTiles() %>%
  setView(lng=rwanda$longitude, lat=rwanda$latitude, zoom=8) %>%
  addCircleMarkers(lng=ss$lon, lat=ss$lat, 
                   radius= ifelse(ss$client==1, 10,6),
                   color = pal(ss$client),
clusterOptions = markerClusterOptions(disableClusteringAtZoom=13, spiderfyOnMaxZoom=FALSE))

map

Summary statistics

Table of final baseline breakdown

count <- d %>% group_by(district) %>% 
  dplyr::summarize(
    t.count = sum(ifelse(client==1,1,0)),
    c.count = sum(ifelse(client==0,1,0)),
    total = n()
  ) %>% ungroup()

count <- as.data.frame(count)
write.csv(count, file=paste(od, "final rw sample breakdown.csv", sep="/"), row.names=F)
as.data.frame(count)

##        district t.count c.count total
## 1   Gatsibo_LWH      58      59   117
## 2  Gatsibo_NLWH      87      81   168
## 3      Gisagara      46      46    92
## 4          Huye     114     115   229
## 5       Karongi     163     159   322
## 6       Kayonza      55      58   113
## 7      Mugonero     131     129   260
## 8     Nyamagabe      56      56   112
## 9    Nyamasheke     147     146   293
## 10       Nyanza      46      46    92
## 11    Nyaruguru      46      46    92
## 12      Rutsiro     165     167   332
## 13    Rwamagana     110     111   221

Baseline balance

Let’s see how balanced our farmers are in terms of demographic variables. Tubura farmers were selected based on (list criteria) and control farmers in the same area tha fit the same criteria were also selected. No matching process has been performed to identify the control farmers that most closely resemble the Tubura farmers in the sample. These results are entirely reflecting the balance inherent in the identification process, not any statistical matching of treatment and control.

out.list <- c("female", "age", "hhsize", "own", "field.size",
              "n_season_fert", "n_season_compost", "n_season_lime", "n_season_fallow", "n_seasons_leg_1", "n_seasons_leg_2", "m3.Ca", "m3.Mg", "pH", "Total.C", "Total.N")

output <- do.call(rbind, lapply(out.list, function(x) {
  
  out <- t.test(d[,x] ~ d[,"client"], data=d)
  tab <- data.frame(out[[5]][[1]], out[[5]][[2]], out[3])
  tab[,1:2] <- round(tab[,1:2],3)
  names(tab) <- c(names(out[[5]]), "pvalue")
  return(tab)
}))

# use p.adjust with bonferroni correction
output$pvalue <- p.adjust(output$pvalue, method="fdr")
rownames(output) <- out.list
output <- output[order(output$pvalue),]
output$pvalue <- ifelse(output[, 3] < 0.001, "< 0.001", round(output[, 3], 3)) 


colnames(output) <- c("Non-Tubura", "Tubura Client", "p-value") 

print(kable(output))

	Non-Tubura	Tubura Client	p-value
n_season_fert	0.833	3.263	< 0.001
female	0.649	0.493	< 0.001
age	48.088	44.021	< 0.001
hhsize	4.894	5.418	< 0.001
n_season_lime	0.132	0.228	< 0.001
own	0.957	0.932	0.023
n_season_compost	5.523	5.818	0.127
n_season_fallow	0.569	0.690	0.128
Total.N	0.158	0.156	0.128
m3.Ca	893.791	858.994	0.17
m3.Mg	211.819	203.847	0.17
field.size	601.671	667.734	0.206
Total.C	2.121	2.098	0.328
pH	5.555	5.533	0.377
n_seasons_leg_1	2.135	2.228	0.424
n_seasons_leg_2	3.353	5.400	0.454

#write table
write.csv(output, file=paste(od, "baseline balance.csv", sep="/"), row.names=T)

Overall balance interpretation

Demographic variables We are not well balanced along the main demographic variables we collected, sex, age and HH size. For the purposes of inference we can test some matching algorithms to improve the match between Tubura and control farmers.

Agricultural practice variables We are decently balanced along agricultural practice variables. Our course of action here is similiar to our options with the demographic variables.

Soil Variables We are balanced on the primary soil variables of interest betwen our Tubura farmers and the comparison farmers.

Baseline balance by district

dist.output <- do.call(rbind, lapply(split(d, d$district), function(x) {
  
  tab <- do.call(rbind, lapply(out.list, function(y) {
    
    out <- t.test(x[,y] ~ x[,"client"], data=x)
    tab <- data.frame(out[[5]][[1]], out[[5]][[2]], out[3])
    tab[,1:2] <- round(tab[,1:2],3)
    names(tab) <- c(names(out[[5]]), "pvalue")
    #tab[,3] <- p.adjust(tab[,3], method="holm")
    #tab[,3] <- ifelse(tab[,3] < 0.001, "< 0.001", round(tab[,3],3))
    #print(tab)
    return(tab)
  }))
  
  return(data.frame(district = unique(x$district), tab))
}))

rownames(dist.output) <- NULL
dist.output$variable <- rep(out.list,length(unique(d$district)))    

# order variables 
dist.output <- dist.output[, c(1, 5, 2:4)]
dist.output$pvalue <- p.adjust(dist.output$pvalue, method="fdr")
dist.output <- dist.output[order(dist.output$pvalue),]

dist.output$pvalue <- ifelse(dist.output$pvalue < 0.001, "< 0.001", round(dist.output$pvalue,3))
colnames(dist.output) <- c("District", "Varible", "Non-Tubura", "Tubura Client", "p-value") 

print(kable(dist.output))

	District	Varible	Non-Tubura	Tubura Client	p-value
70	Karongi	n_season_fert	0.447	3.785	< 0.001
102	Mugonero	n_season_fert	0.597	4.313	< 0.001
182	Rutsiro	n_season_fert	1.066	4.200	< 0.001
134	Nyamasheke	n_season_fert	1.507	5.068	< 0.001
198	Rwamagana	n_season_fert	1.054	2.645	< 0.001
54	Huye	n_season_fert	0.322	2.246	< 0.001
22	Gatsibo_NLWH	n_season_fert	0.296	1.517	< 0.001
118	Nyamagabe	n_season_fert	1.554	4.000	< 0.001
136	Nyamasheke	n_season_lime	0.041	0.327	< 0.001
86	Kayonza	n_season_fert	0.776	2.073	< 0.001
194	Rwamagana	age	52.072	44.245	0.001
131	Nyamasheke	hhsize	4.685	5.701	0.003
65	Karongi	female	0.667	0.466	0.004
163	Nyaruguru	hhsize	4.717	6.217	0.004
45	Gisagara	m3.Mg	241.171	190.036	0.006
50	Huye	age	49.400	43.395	0.009
44	Gisagara	m3.Ca	1203.823	895.928	0.01
145	Nyanza	female	0.543	0.217	0.012
150	Nyanza	n_season_fert	0.152	1.326	0.019
18	Gatsibo_NLWH	age	46.210	39.897	0.019
17	Gatsibo_NLWH	female	0.556	0.322	0.021
2	Gatsibo_LWH	age	49.949	41.931	0.027
113	Nyamagabe	female	0.750	0.482	0.03
81	Kayonza	female	0.672	0.400	0.03
20	Gatsibo_NLWH	own	1.000	0.908	0.031
104	Mugonero	n_season_lime	0.023	0.176	0.031
193	Rwamagana	female	0.739	0.555	0.031
1	Gatsibo_LWH	female	0.492	0.241	0.034
179	Rutsiro	hhsize	4.844	5.624	0.034
99	Mugonero	hhsize	5.054	5.802	0.049
98	Mugonero	age	49.140	44.290	0.067
161	Nyaruguru	female	0.652	0.391	0.077
48	Gisagara	Total.N	0.154	0.142	0.079
184	Rutsiro	n_season_lime	0.096	0.327	0.082
47	Gisagara	Total.C	2.005	1.816	0.086
135	Nyamasheke	n_season_compost	5.521	6.544	0.089
59	Huye	n_seasons_leg_2	5.278	3.667	0.096
138	Nyamasheke	n_seasons_leg_1	1.658	2.327	0.101
166	Nyaruguru	n_season_fert	1.065	2.130	0.104
35	Gisagara	hhsize	4.326	5.348	0.113
6	Gatsibo_LWH	n_season_fert	1.475	2.552	0.121
51	Huye	hhsize	4.574	5.132	0.141
115	Nyamagabe	hhsize	4.696	5.482	0.141
41	Gisagara	n_season_fallow	0.087	0.500	0.184
43	Gisagara	n_seasons_leg_2	3.283	2.370	0.184
148	Nyanza	own	1.000	0.913	0.197
196	Rwamagana	own	0.973	0.909	0.197
46	Gisagara	pH	5.945	5.759	0.213
27	Gatsibo_NLWH	n_seasons_leg_2	3.889	3.046	0.22
38	Gisagara	n_season_fert	0.348	1.087	0.22
72	Karongi	n_season_lime	0.013	0.098	0.225
155	Nyanza	n_seasons_leg_2	3.478	2.130	0.225
88	Kayonza	n_season_lime	0.707	0.527	0.226
201	Rwamagana	n_season_fallow	0.712	1.218	0.226
114	Nyamagabe	age	48.875	43.768	0.229
176	Nyaruguru	Total.N	0.170	0.161	0.238
205	Rwamagana	m3.Mg	293.168	273.526	0.298
146	Nyanza	age	50.152	44.717	0.335
33	Gisagara	female	0.609	0.435	0.339
66	Karongi	age	47.384	44.681	0.339
95	Kayonza	Total.C	2.556	2.400	0.343
82	Kayonza	age	46.500	42.345	0.351
64	Huye	Total.N	0.148	0.143	0.353
23	Gatsibo_NLWH	n_season_compost	3.420	2.632	0.36
92	Kayonza	m3.Ca	1863.601	1664.716	0.36
183	Rutsiro	n_season_compost	7.593	8.176	0.36
11	Gatsibo_LWH	n_seasons_leg_2	2.898	1.983	0.411
185	Rutsiro	n_season_fallow	0.287	0.473	0.431
49	Huye	female	0.591	0.500	0.446
84	Kayonza	own	0.897	0.964	0.446
85	Kayonza	field.size	423.776	664.236	0.446
96	Kayonza	Total.N	0.187	0.180	0.446
108	Mugonero	m3.Ca	604.767	555.744	0.446
122	Nyamagabe	n_seasons_leg_1	1.125	1.625	0.446
168	Nyaruguru	n_season_lime	0.000	0.043	0.446
177	Rutsiro	female	0.623	0.545	0.446
190	Rutsiro	pH	5.338	5.264	0.446
207	Rwamagana	Total.C	2.232	2.169	0.446
24	Gatsibo_NLWH	n_season_lime	0.025	0.069	0.455
158	Nyanza	pH	5.999	6.105	0.466
164	Nyaruguru	own	0.935	0.848	0.466
203	Rwamagana	n_seasons_leg_2	1.685	0.536	0.466
174	Nyaruguru	pH	5.210	5.319	0.472
71	Karongi	n_season_compost	6.553	7.074	0.478
68	Karongi	own	0.981	0.957	0.502
130	Nyamasheke	age	48.123	45.898	0.502
156	Nyanza	m3.Ca	987.213	1083.103	0.502
188	Rutsiro	m3.Ca	683.185	631.247	0.502
58	Huye	n_seasons_leg_1	1.043	1.386	0.522
173	Nyaruguru	m3.Mg	138.204	151.996	0.522
191	Rutsiro	Total.C	2.304	2.240	0.525
110	Mugonero	pH	5.242	5.181	0.525
157	Nyanza	m3.Mg	210.773	230.037	0.525
67	Karongi	hhsize	4.912	5.172	0.531
175	Nyaruguru	Total.C	2.229	2.140	0.542
142	Nyamasheke	pH	5.123	5.179	0.562
3	Gatsibo_LWH	hhsize	5.763	5.362	0.61
42	Gisagara	n_seasons_leg_1	2.870	2.304	0.61
56	Huye	n_season_lime	0.113	0.035	0.61
204	Rwamagana	m3.Ca	1376.064	1298.489	0.61
165	Nyaruguru	field.size	495.239	570.022	0.621
4	Gatsibo_LWH	own	1.000	0.983	0.622
52	Huye	own	0.991	0.974	0.622
93	Kayonza	m3.Mg	357.168	336.861	0.622
100	Mugonero	own	0.915	0.947	0.622
128	Nyamagabe	Total.N	0.165	0.169	0.622
181	Rutsiro	field.size	430.156	584.327	0.622
97	Mugonero	female	0.713	0.656	0.627
79	Karongi	Total.C	1.832	1.877	0.637
189	Rutsiro	m3.Mg	174.194	163.840	0.637
8	Gatsibo_LWH	n_season_lime	0.322	0.500	0.645
37	Gisagara	field.size	559.261	493.957	0.645
94	Kayonza	pH	6.203	6.129	0.645
139	Nyamasheke	n_seasons_leg_2	3.575	24.796	0.645
187	Rutsiro	n_seasons_leg_2	2.593	2.036	0.646
107	Mugonero	n_seasons_leg_2	4.031	3.511	0.651
192	Rutsiro	Total.N	0.160	0.157	0.651
206	Rwamagana	pH	5.873	5.817	0.651
5	Gatsibo_LWH	field.size	916.441	776.345	0.652
127	Nyamagabe	Total.C	2.266	2.336	0.652
101	Mugonero	field.size	393.124	441.359	0.655
171	Nyaruguru	n_seasons_leg_2	3.370	5.326	0.655
208	Rwamagana	Total.N	0.178	0.175	0.655
25	Gatsibo_NLWH	n_season_fallow	0.543	0.736	0.662
129	Nyamasheke	female	0.692	0.646	0.678
57	Huye	n_season_fallow	0.487	0.675	0.684
133	Nyamasheke	field.size	580.130	787.527	0.684
147	Nyanza	hhsize	4.891	5.261	0.684
172	Nyaruguru	m3.Ca	615.230	665.044	0.687
144	Nyamasheke	Total.N	0.167	0.165	0.69
117	Nyamagabe	field.size	282.643	310.929	0.7
34	Gisagara	age	46.848	44.761	0.703
109	Mugonero	m3.Mg	169.468	159.707	0.719
10	Gatsibo_LWH	n_seasons_leg_1	4.678	4.345	0.72
69	Karongi	field.size	446.088	490.788	0.72
77	Karongi	m3.Mg	269.452	254.229	0.72
21	Gatsibo_NLWH	field.size	1459.901	1306.069	0.744
55	Huye	n_season_compost	4.878	5.211	0.744
12	Gatsibo_LWH	m3.Ca	1139.996	1206.971	0.757
80	Karongi	Total.N	0.142	0.144	0.757
90	Kayonza	n_seasons_leg_1	2.155	1.982	0.757
153	Nyanza	n_season_fallow	0.870	1.130	0.757
180	Rutsiro	own	0.934	0.915	0.757
39	Gisagara	n_season_compost	3.957	4.326	0.758
78	Karongi	pH	5.477	5.441	0.758
199	Rwamagana	n_season_compost	3.748	4.018	0.759
106	Mugonero	n_seasons_leg_1	1.186	1.336	0.769
9	Gatsibo_LWH	n_season_fallow	0.288	0.397	0.769
19	Gatsibo_NLWH	hhsize	5.160	5.333	0.769
36	Gisagara	own	0.870	0.826	0.769
91	Kayonza	n_seasons_leg_2	1.259	1.091	0.769
116	Nyamagabe	own	0.982	0.964	0.769
119	Nyamagabe	n_season_compost	7.518	7.857	0.769
169	Nyaruguru	n_season_fallow	0.261	0.370	0.769
178	Rutsiro	age	44.617	43.685	0.769
120	Nyamagabe	n_season_lime	0.393	0.500	0.78
61	Huye	m3.Mg	190.397	186.200	0.789
141	Nyamasheke	m3.Mg	147.629	153.726	0.789
53	Huye	field.size	567.922	599.096	0.8
123	Nyamagabe	n_seasons_leg_2	2.929	3.161	0.8
29	Gatsibo_NLWH	m3.Mg	254.332	246.971	0.814
132	Nyamasheke	own	0.945	0.932	0.814
140	Nyamasheke	m3.Ca	590.765	613.771	0.814
167	Nyaruguru	n_season_compost	6.043	5.696	0.814
149	Nyanza	field.size	766.217	853.359	0.818
170	Nyaruguru	n_seasons_leg_1	2.348	2.043	0.819
154	Nyanza	n_seasons_leg_1	2.283	2.543	0.828
197	Rwamagana	field.size	842.054	892.855	0.831
202	Rwamagana	n_seasons_leg_1	1.568	1.682	0.831
126	Nyamagabe	pH	5.022	5.002	0.836
200	Rwamagana	n_season_lime	0.324	0.355	0.836
60	Huye	m3.Ca	870.054	853.743	0.847
62	Huye	pH	5.665	5.684	0.848
30	Gatsibo_NLWH	pH	6.061	6.038	0.852
103	Mugonero	n_season_compost	6.070	6.229	0.872
137	Nyamasheke	n_season_fallow	0.664	0.599	0.872
76	Karongi	m3.Ca	803.893	787.032	0.89
16	Gatsibo_LWH	Total.N	0.146	0.148	0.916
13	Gatsibo_LWH	m3.Mg	235.470	239.641	0.924
14	Gatsibo_LWH	pH	6.119	6.138	0.924
15	Gatsibo_LWH	Total.C	1.866	1.887	0.924
63	Huye	Total.C	1.919	1.910	0.924
105	Mugonero	n_season_fallow	0.915	0.863	0.924
121	Nyamagabe	n_season_fallow	0.304	0.268	0.924
124	Nyamagabe	m3.Ca	449.585	456.505	0.924
125	Nyamagabe	m3.Mg	108.307	106.662	0.924
143	Nyamasheke	Total.C	2.285	2.298	0.924
159	Nyanza	Total.C	1.778	1.761	0.924
186	Rutsiro	n_seasons_leg_1	3.479	3.388	0.924
28	Gatsibo_NLWH	m3.Ca	1246.188	1230.161	0.926
75	Karongi	n_seasons_leg_2	3.956	3.816	0.926
195	Rwamagana	hhsize	4.982	4.927	0.926
83	Kayonza	hhsize	5.155	5.091	0.928
7	Gatsibo_LWH	n_season_compost	5.780	5.672	0.938
112	Mugonero	Total.N	0.153	0.154	0.938
89	Kayonza	n_season_fallow	0.483	0.455	0.947
160	Nyanza	Total.N	0.134	0.134	0.957
31	Gatsibo_NLWH	Total.C	1.994	2.002	0.959
151	Nyanza	n_season_compost	3.326	3.261	0.966
32	Gatsibo_NLWH	Total.N	0.158	0.157	0.977
26	Gatsibo_NLWH	n_seasons_leg_1	1.556	1.540	0.978
73	Karongi	n_season_fallow	0.843	0.834	0.978
74	Karongi	n_seasons_leg_1	2.497	2.485	0.978
87	Kayonza	n_season_compost	3.534	3.564	0.978
111	Mugonero	Total.C	2.203	2.206	0.978
162	Nyaruguru	age	48.304	48.457	0.978
40	Gisagara	n_season_lime	0.022	0.022	1
152	Nyanza	n_season_lime	0.000	0.000	NA

District balance interpretation

Demographic variables interpretation here.

Agricultural practice variables interpretation here

Soil Variables interpretation here

write.csv(dist.output, file=paste(od, "district balance.csv", sep="/"), row.names=T)

Baseline balance by Tubura tenure

Look at farmers by duration of tenure farming with Tubura. We want to understand, at least with an initial naive baseline sense, what is the cumulative effect of Tubura practices on soil health outcomes?

We will look only at current Tubura farmers and compare first year farmers to farmers with more experience with Tubura.

oafOnly <- d[which(d$client==0 & d$total.seasons>=1),]

nTenure <- oafOnly %>% group_by(total.seasons) %>% 
  summarize(
    n = n()
  ) %>% ungroup() %>% as.data.frame()
nTenure$val <- paste(nTenure$total.seasons, " (", "n = ", nTenure$n, ")", sep = "")

for(i in 1:length(soilVars)){
print(
  ggplot(oafOnly, aes(x=as.factor(total.seasons), y=oafOnly[,soilVars[i]])) + 
    geom_boxplot() +
    scale_x_discrete(labels=nTenure$val) + 
    theme(legend.position = "bottom", axis.text.x = element_text(angle = 45, hjust = 1)) +
    labs(x="Tubura Tenure", y=soilVars[i], title = paste("RW baseline soil by tenure - ", soilVars[i], sep = ""))
  )  
}

Tenure summaries

tenureSum <- aggregate(oafOnly[,out.list], by=list(oafOnly$total.seasons), function(x){
  round(mean(x, na.rm=T),2)
})
tenureSum <- as.data.frame(t(tenureSum))
colnames(tenureSum) <- c(paste(seq(1,11,1), " seas.", sep = ""), "13 seas.")

print(kable(tenureSum))

	1 seas.	2 seas.	3 seas.	4 seas.	5 seas.	6 seas.	7 seas.	8 seas.	9 seas.	10 seas.	11 seas.	13 seas.
Group.1	1.00	2.00	3.00	4.00	5.00	6.00	7.00	8.00	9.00	10.00	11.00	13.00
female	0.70	0.61	0.67	0.65	0.64	0.58	0.75	0.33	0.33	0.75	0.67	0.00
age	48.77	46.43	46.46	48.96	42.73	43.83	42.12	52.33	36.00	48.50	42.00	52.00
hhsize	5.30	5.40	5.71	4.91	6.09	5.25	5.50	5.83	6.67	6.50	8.67	6.00
own	0.92	0.97	1.00	1.00	0.91	1.00	1.00	0.83	1.00	1.00	1.00	1.00
field.size	564.72	595.76	390.17	547.13	976.18	289.17	346.75	602.33	256.00	241.00	334.67	480.00
n_season_fert	1.03	1.27	3.17	1.65	1.82	2.83	2.38	5.33	2.67	3.75	0.33	10.00
n_season_compost	5.48	5.61	6.58	4.43	5.82	6.50	6.75	8.33	10.00	8.25	4.67	10.00
n_season_lime	0.27	0.17	0.25	0.09	0.18	0.33	0.00	0.17	0.00	0.00	0.00	0.00
n_season_fallow	0.53	0.74	0.58	1.00	0.45	0.50	0.88	0.00	0.00	0.00	1.33	0.00
n_seasons_leg_1	2.12	2.14	1.96	2.00	1.55	1.25	0.62	3.00	4.00	2.25	4.33	1.00
n_seasons_leg_2	3.13	2.85	4.50	2.57	6.27	2.33	5.88	3.50	3.33	5.25	0.00	9.00
m3.Ca	1127.45	946.96	1034.46	686.67	678.56	625.67	870.40	443.64	1153.25	483.06	746.88	632.20
m3.Mg	247.35	226.65	252.39	165.35	153.59	138.80	217.69	120.77	307.42	153.92	177.55	224.80
pH	5.72	5.56	5.70	5.20	5.34	5.34	5.64	5.10	5.87	5.18	5.50	5.54
Total.C	2.13	2.19	2.19	2.36	2.01	2.06	1.83	2.36	1.85	2.26	1.77	2.06
Total.N	0.16	0.16	0.16	0.17	0.15	0.15	0.14	0.16	0.15	0.15	0.13	0.16

Tenure balance

We’re defining Tubura tenure as having 3 or more seasons of experience farming with Tubura. We draw the line at 3 seasons as three seasons of fertilizer use is approximately when we’d expect fertilizer to start to have a detrimental effect on soil health.

oafOnly$tenured <- ifelse(oafOnly$total.seasons>=3,1,0)

tenure <- do.call(rbind, lapply(out.list, function(x) {
  
  out <- t.test(oafOnly[,x] ~ oafOnly[,"tenured"], data=oafOnly)
  tab <- data.frame(out[[5]][[1]], out[[5]][[2]], out[3])
  tab[,1:2] <- round(tab[,1:2],3)
  names(tab) <- c(names(out[[5]]), "pvalue")
  return(tab)
}))

# use p.adjust with bonferroni correction
tenure$pvalue <- p.adjust(tenure$pvalue, method="fdr")
rownames(tenure) <- out.list
tenure <- tenure[order(tenure$pvalue),]
tenure$pvalue <- ifelse(tenure[, 3] < 0.001, "< 0.001", round(tenure[, 3], 3)) 


colnames(tenure) <- c("Non-Tubura", "Tubura Client", "p-value") 

print(kable(tenure))

	Non-Tubura	Tubura Client	p-value
n_season_fert	1.141	2.663	< 0.001
m3.Ca	1046.351	773.500	0.001
m3.Mg	238.052	189.232	0.004
pH	5.648	5.424	0.005
own	0.943	0.979	0.263
Total.N	0.162	0.156	0.263
n_season_compost	5.537	6.242	0.295
n_season_lime	0.225	0.158	0.324
n_seasons_leg_2	3.004	3.916	0.324
hhsize	5.348	5.653	0.4
age	47.718	45.979	0.415
field.size	578.672	481.684	0.415
female	0.661	0.621	0.618
n_seasons_leg_1	2.128	1.926	0.625
n_season_fallow	0.621	0.621	1
Total.C	2.154	2.150	1

Tenured v. new balance interpretation

Demographic variables We are well balanced along demographic variables.

Agricultural practice variables Not surprisingly, Tubura farmers have more cumulative years of fertilizer use than current non-Tubura farmers. While that difference is signficant, it is realistically only a single season of fertilizer use different.

Interestingly, non-Tubura farmers reported using more lime than current Tubura farmers. This

Soil Variables Soil pH, calcium and magnesium levels are lower for tenured Tubura farmers. This is consistent with the hypothesis that increaesd fertilizer use leads to an increaese in soil acidity.

Analysis of agronomic practices contributing to soil health outcomes

Here’s where we’ll look at the contribution of fertilizer, lime and cultivation practices on soil health outcomes. This analysis will be come richer as we gain longitudinal measures. I caution that we cannot treat these relationships as causal. The direction of causality is not clearly delineated in the data or the study design. However, we can identify meaningful connections between practices and outcomes through this analysis to generate new hypotheses for field testing.

I’m going to start with behaviors by sections and then move to a more comprehensive model including multiple practices. All models will include controls for site to account for local variation and field officer behavior.

Agronomic Behaviors

Check for multicollinearity before adding number of seasons of agronomic inputs on the same side of the regression.

suppressMessages(library(stargazer))

inputUse <- c("n_season_fert","n_season_compost", "n_season_lime", "n_season_fallow")

cor(d[,inputUse], use="complete.obs")

##                  n_season_fert n_season_compost n_season_lime
## n_season_fert       1.00000000       0.35646933    0.17075604
## n_season_compost    0.35646933       1.00000000    0.03828723
## n_season_lime       0.17075604       0.03828723    1.00000000
## n_season_fallow    -0.06439632      -0.16923273   -0.01116383
##                  n_season_fallow
## n_season_fert        -0.06439632
## n_season_compost     -0.16923273
## n_season_lime        -0.01116383
## n_season_fallow       1.00000000

Interpretation: The strongest correlation between the input use intensity variables is between seasons of fertilizer and compost use, ~0.35. While this is on the higher end it’s not necessarily cause for alarm.

inputUse <- paste(c("n_season_fert","n_season_compost", "n_season_lime", "n_season_fallow"), collapse= " + ")

list1 <- lapply(soilVars, function(x){
  mod <- lm(as.formula(paste("d[,x] ~", inputUse, "+ as.factor(cell)", sep="")), data=d)
  return(mod)
})

stargazer(list1, type="html", 
          title = "2016A Rwanda Soil Health Baseline - Naive Agronomic Practice Models",
          covariate.labels = c("Seasons of Fertilizer", "Seasons of Compost", 
                               "Seasons of Lime", "Seasons of Fallow"),
          dep.var.caption = "",
          dep.var.labels = "",
          column.labels = c(gsub("m3.","", soilVars)),
          notes = "Includes FE for cell",
          omit=c("cell"), out=paste(od, "rw_baseline_agprac.htm", sep="/"))

2016A Rwanda Soil Health Baseline - Naive Agronomic Practice Models

	Ca	Mg	pH	Total.N	Total.C
	(1)	(2)	(3)	(4)	(5)
Seasons of Fertilizer	-5.351	-1.230*	-0.001	-0.0004**	-0.003
	(3.266)	(0.703)	(0.003)	(0.0002)	(0.003)
Seasons of Compost	1.364	0.363	0.003	0.0002	0.002
	(2.635)	(0.567)	(0.003)	(0.0001)	(0.003)
Seasons of Lime	41.646***	8.175***	0.022	0.002**	0.023
	(14.233)	(3.065)	(0.014)	(0.001)	(0.015)
Seasons of Fallow	-19.729***	-3.674***	-0.028***	0.0004	0.009
	(5.196)	(1.119)	(0.005)	(0.0003)	(0.005)
Constant	589.376	63.444	4.674***	0.200***	3.298***
	(381.191)	(82.085)	(0.366)	(0.021)	(0.390)
Observations	2,443	2,443	2,443	2,443	2,443
R2	0.557	0.592	0.616	0.502	0.458
Adjusted R2	0.517	0.555	0.581	0.457	0.409
Residual Std. Error (df = 2238)	381.045	82.054	0.366	0.021	0.390
F Statistic (df = 204; 2238)	13.809***	15.941***	17.628***	11.059***	9.277***
Note:	p<0.1; p<0.05; p<0.01
	Includes FE for cell

Interpretation The naive model suggests that when we include site level fixed effects, duration of agronomic practices don’t have a big effect on soil health outcomes. However, some of the practice intensity variables are not well distributed. Let’s take a look at a log transformation. I’m adding one to the variables as to not end up with lots of Inf values.

agPrac <- c(names(d[grep('n_season_', names(d))]))

for(i in 1:length(agPrac)){
  print(
    ggplot(d, aes(x=d[,agPrac[i]])) + geom_histogram(binwidth = 1) +
      labs(x = agPrac[i])
        )
}

# since these are all skewed, consider a log transform 
for(i in 1:length(agPrac)){
  print(
    ggplot(d, aes(x=log(d[,agPrac[i]]+1))) + geom_histogram(binwidth = 1) +
      labs(x = agPrac[i])
        )
}

d$logFert <- log(d$n_season_fert+1)
d$logCompost <- log(d$n_season_compost+1)
d$logLime <- log(d$n_season_lime+1)
d$logFallow <- log(d$n_season_fallow+1)

Let’s look at the log results: See here for guidance on intepreting log transformed right hand side variables.

How to interpret RHS log transform: For a linear multivariate OLS regression, we say “a one unit increase in X causes a (coefficient) change in Y.” For a linear-log regression where the X variable is log transformed, we say a L percent change in X leads to a (coefficient*L) change in Y.

logVars <- paste(names(d[grep("log", names(d))]), collapse=" + ")

list2 <- lapply(soilVars, function(x){
  mod <- lm(as.formula(paste("d[,x] ~",  logVars, "+ as.factor(cell)", sep="")), data=d)
  return(mod)
})

list2b <- lapply(soilVars, function(x){
  mod <- lm(as.formula(paste("d[,x] ~",  logVars, sep="")), data=d)
  return(mod)
})

suppressWarnings(
  stargazer(list2, list2b, type="html", 
          title = "2016A Rwanda Soil Health Baseline - Log Agronomic Practice Models",
          covariate.labels = c("Seasons of Fertilizer (log)", "Seasons of Compost (log)", "Seasons of Lime (log)", "Seasons of Fallow (log)"),
          column.labels = c(rep(gsub("m3.","", soilVars),2)),
          dep.var.caption = "",
          dep.var.labels = c("",""),
          add.lines = list(c("Cell FE?", rep("Yes", 5), rep("No", 5))),
          notes = "Includes FE for cell",
          omit=c("cell"), out=paste(od, "rw_baseline_agprac_log.htm", sep="/"))
)

2016A Rwanda Soil Health Baseline - Log Agronomic Practice Models

	Ca	Mg	pH	Total.N	Total.C	Ca	Mg	pH	Total.N	Total.C
	(1)	(2)	(3)	(4)	(5)	(6)	(7)	(8)	(9)	(10)
Seasons of Fertilizer (log)	-23.685**	-5.633**	-0.008	-0.002**	-0.013	-53.105***	-7.185**	-0.046***	-0.002**	-0.017
	(11.366)	(2.449)	(0.011)	(0.001)	(0.012)	(14.518)	(3.312)	(0.015)	(0.001)	(0.014)
Seasons of Compost (log)	7.778	1.726	0.016	0.001	0.008	-96.407***	-14.142***	-0.111***	0.0003	0.028**
	(11.964)	(2.578)	(0.011)	(0.001)	(0.012)	(14.382)	(3.281)	(0.015)	(0.001)	(0.014)
Seasons of Lime (log)	122.237***	22.996***	0.063**	0.005***	0.068**	312.150***	41.254***	0.204***	0.014***	0.188***
	(32.098)	(6.917)	(0.031)	(0.002)	(0.033)	(38.120)	(8.697)	(0.039)	(0.002)	(0.036)
Seasons of Fallow (log)	-72.103***	-13.697***	-0.103***	0.001	0.021	-125.822***	-26.255***	-0.169***	0.002	0.034*
	(15.227)	(3.281)	(0.015)	(0.001)	(0.016)	(19.660)	(4.485)	(0.020)	(0.001)	(0.019)
Constant	582.312	62.119	4.662***	0.199***	3.293***	1,075.500***	239.116***	5.785***	0.156***	2.047***
	(380.303)	(81.949)	(0.365)	(0.021)	(0.390)	(26.342)	(6.010)	(0.027)	(0.001)	(0.025)
Cell FE?	Yes	Yes	Yes	Yes	Yes	No	No	No	No	No
Observations	2,443	2,443	2,443	2,443	2,443	2,443	2,443	2,443	2,443	2,443
R2	0.560	0.594	0.620	0.502	0.458	0.061	0.030	0.060	0.021	0.014
Adjusted R2	0.520	0.557	0.585	0.457	0.409	0.060	0.028	0.058	0.019	0.012
Residual Std. Error	379.815 (df = 2238)	81.843 (df = 2238)	0.364 (df = 2238)	0.021 (df = 2238)	0.390 (df = 2238)	531.648 (df = 2438)	121.288 (df = 2438)	0.549 (df = 2438)	0.029 (df = 2438)	0.504 (df = 2438)
F Statistic	13.970*** (df = 204; 2238)	16.079*** (df = 204; 2238)	17.886*** (df = 204; 2238)	11.078*** (df = 204; 2238)	9.285*** (df = 204; 2238)	39.691*** (df = 4; 2438)	18.661*** (df = 4; 2438)	38.608*** (df = 4; 2438)	13.070*** (df = 4; 2438)	8.376*** (df = 4; 2438)
Note:	p<0.1; p<0.05; p<0.01
	Includes FE for cell

# a 10 percent increase in x leads to B1*.1 change in Y
logTrans <- do.call(cbind, lapply(list2, function(x){
  coeff = x$coefficients[2:5]
  tenPercent = round(coeff*.1, 5)
  names(tenPercent) <- paste("10% increase in ", gsub("log","", names(tenPercent)), " leads to:", sep="")
  return(tenPercent)
}))
colnames(logTrans) <- soilVars

print(kable(logTrans))

	m3.Ca	m3.Mg	pH	Total.N	Total.C
10% increase in Fert leads to:	-2.36850	-0.56333	-0.00079	-0.00015	-0.00132
10% increase in Compost leads to:	0.77779	0.17263	0.00158	0.00007	0.00076
10% increase in Lime leads to:	12.22368	2.29962	0.00629	0.00050	0.00676
10% increase in Fallow leads to:	-7.21034	-1.36970	-0.01026	0.00009	0.00210

Interpretation: When we transform the variables to log, the data starts to tell a more coherent story, at least directionally. If we remove the district FE, the coefficients gain significance.

• Additional seasons of fertilizer use relates to a decrease in soil N and C.
• Seasons of compost and lime have the opposite, positive effect on soil N.
• Unsurprisingly, soil health metrics are poorer for soils on which more fertilizer has been used and lime has not been used.

Tenure with One Acre Fund

Let’s look first at a naive model of One Acre Fund tenure on soil health. Remember: these data are not longitudinal! These data are not longitudinal and reflect farmer selection into One Acre Fund. While these models will try to be both robust and parsimonious, we will inevitabily suffer omitted variable bias due to a lack of an instrument.

list3 <- lapply(soilVars, function(x){
  mod <- lm(as.formula(paste("d[,x] ~",  "total.seasons + as.factor(cell)", sep="")), data=d)
  return(mod)
})

stargazer(list3, type="html", 
          title = "2016A Rwanda Soil Health Baseline - Naive Tenure Models",
          covariate.labels = c("OAF Tenure"),
          dep.var.caption = "",
          dep.var.labels = "",
          column.labels = c(gsub("m3.","", soilVars)),
          notes = "Includes FE for cell",
          omit=c("cell"), out=paste(od, "rw_baseline_tenure.htm", sep="/"))

2016A Rwanda Soil Health Baseline - Naive Tenure Models

	Ca	Mg	pH	Total.N	Total.C
	(1)	(2)	(3)	(4)	(5)
OAF Tenure	-0.788	-0.122	0.002	-0.0002	-0.001
	(2.810)	(0.604)	(0.003)	(0.0002)	(0.003)
Constant	596.407	65.140	4.683***	0.201***	3.308***
	(382.946)	(82.379)	(0.369)	(0.021)	(0.390)
Observations	2,443	2,443	2,443	2,443	2,443
R2	0.552	0.589	0.610	0.500	0.457
Adjusted R2	0.512	0.552	0.575	0.455	0.408
Residual Std. Error (df = 2241)	382.905	82.370	0.369	0.021	0.390
F Statistic (df = 201; 2241)	13.757***	15.955***	17.423***	11.155***	9.377***
Note:	p<0.1; p<0.05; p<0.01
	Includes FE for cell

Interpretation: The naive One Acre Fund tenure model suggest that across the board that additional years of 1AF practices have a negative effect on soil health parameters. Let’s combine 1AF tenure with the agronomic practices model above to build a more robust model:

list4 <- lapply(soilVars, function(x){
  mod <- lm(as.formula(paste("d[,x] ~",  logVars, "+ total.seasons + as.factor(cell)", sep="")), data=d)
  return(mod)
})

stargazer(list4, type="html", 
          title = "2016A Rwanda Soil Health Baseline - Ag Practice and Tenure",
          covariate.labels = c("Seasons of Fertilizer (log)", "Seasons of Compost (log)", "Seasons of Lime (log)", "Seasons of Fallow (log)", "OAF Tenure"),
          dep.var.caption = "",
          dep.var.labels = "",
          column.labels = c(gsub("m3.","", soilVars)),
          notes = "Includes FE for cell",
          omit=c("cell"), out=paste(od, "rw_baseline_ag_tenure.htm", sep="/"))

2016A Rwanda Soil Health Baseline - Ag Practice and Tenure

	Ca	Mg	pH	Total.N	Total.C
	(1)	(2)	(3)	(4)	(5)
Seasons of Fertilizer (log)	-28.649**	-7.229**	-0.017	-0.001*	-0.011
	(13.713)	(2.955)	(0.013)	(0.001)	(0.014)
Seasons of Compost (log)	7.871	1.756	0.016	0.001	0.008
	(11.966)	(2.578)	(0.011)	(0.001)	(0.012)
Seasons of Lime (log)	122.500***	23.081***	0.063**	0.005***	0.068**
	(32.105)	(6.917)	(0.031)	(0.002)	(0.033)
Seasons of Fallow (log)	-72.522***	-13.831***	-0.103***	0.001	0.021
	(15.242)	(3.284)	(0.015)	(0.001)	(0.016)
OAF Tenure	2.215	0.712	0.004	-0.0001	-0.001
	(3.423)	(0.737)	(0.003)	(0.0002)	(0.004)
Constant	577.732	60.646	4.654***	0.199***	3.295***
	(380.418)	(81.964)	(0.365)	(0.021)	(0.390)
Observations	2,443	2,443	2,443	2,443	2,443
R2	0.560	0.595	0.620	0.503	0.458
Adjusted R2	0.520	0.557	0.585	0.457	0.409
Residual Std. Error (df = 2237)	379.864	81.845	0.364	0.021	0.390
F Statistic (df = 205; 2237)	13.900***	16.005***	17.810***	11.022***	9.236***
Note:	p<0.1; p<0.05; p<0.01
	Includes FE for cell

Interpretation: Including agronomic practices and 1AF tenure in the same model dampens the magnitude, but not the significance, of 1AF tenure on soil health outcomes.

Agronomic practices - 15B cultivation practices

Thus far we have looked at aggregated historical plot level practices and their effect on soil health. We also asked farmers about their cultivation practices on their plot in the previous season, 15B. We have more precise information for fertilizer, compost and liming practices for the 15B season.

# this should be kg of fertilizer used in this field. Compost is off the charts. Convert this to compost per sq meter
d$fert_15b_log <- ifelse(d$field_kg_fert1_15b<=20, 
                         log(d$field_kg_fert1_15b+1), NA)

d$field_dim <- d$field_dim1*d$field_dim2

d$compost_15b_sqm <- d$field_kg_compost_15b/d$field_dim
d$compost_15b_sqm_log <- log(d$compost_15b_sqm+1)


# more than 20 kg per are seems like too much.
suppressMessages(qplot(d$fert_15b_log, binwidth=1))

## Warning: Removed 1808 rows containing non-finite values (stat_bin).

suppressMessages(qplot(d$compost_15b_sqm_log, binwidth=1))

## Warning: Removed 143 rows containing non-finite values (stat_bin).

previousSeason <- paste("fert_15b_log", "compost_15b_sqm_log", "as.factor(cell)", sep=" + ")

list5 <- lapply(soilVars, function(x){
  mod <- lm(as.formula(paste("d[,x] ~", previousSeason, sep="")), data=d)
  return(mod)
})

stargazer(list5, type="html", 
          title = "2016A Rwanda Soil Health Baseline - 15B practices",
          covariate.labels = c("Fertilizer Rate (log)", "Compost Rate kg/m^2 (log)"),
          dep.var.caption = "",
          dep.var.labels = "",
          column.labels = c(gsub("m3.","", soilVars)),
          notes = "Includes FE for cell",
          omit=c("cell"), out=paste(od, "rw_baseline_15b_ag.htm", sep="/"))

2016A Rwanda Soil Health Baseline - 15B practices

	Ca	Mg	pH	Total.N	Total.C
	(1)	(2)	(3)	(4)	(5)
Fertilizer Rate (log)	-3.031	-0.559	-0.080**	0.002	0.065*
	(30.767)	(7.255)	(0.033)	(0.002)	(0.038)
Compost Rate kg/m(log)	21.701	13.123	-0.049	0.0001	0.004
	(43.604)	(10.282)	(0.046)	(0.003)	(0.054)
Constant	1,565.244***	317.362***	6.009***	0.189***	2.322***
	(167.238)	(39.437)	(0.177)	(0.011)	(0.209)
Observations	635	635	635	635	635
R2	0.703	0.718	0.697	0.608	0.541
Adjusted R2	0.590	0.609	0.580	0.458	0.364
Residual Std. Error (df = 458)	325.910	76.854	0.345	0.021	0.406
F Statistic (df = 176; 458)	6.173***	6.615***	5.973***	4.043***	3.063***
Note:	p<0.1; p<0.05; p<0.01
	Includes FE for cell

Farmer fertility perception

Let’s look at farmer perceived fertility as a predictor of soil health. We’ll set ‘same fertility’ as the reference category.

d$fertility_qual <- relevel(as.factor(d$general_field_infocompare_fertil), ref="same")

list6 <- lapply(soilVars, function(x){
  mod <- lm(as.formula(paste("d[,x] ~", "+ fertility_qual + as.factor(cell)", sep="")), data=d)
  return(mod)
})


stargazer(list6, type="html", 
          title = "2016A Rwanda Soil Health Baseline - Farmer Perceived Fertility",
          covariate.labels = c("Farmer Opinion - Less Fertile",
                               "Farmer Opinion - More Fertile"),
          dep.var.caption = "",
          dep.var.labels = "",
          column.labels = c(gsub("m3.","", soilVars)),
          notes = "Reference category is same fertility as other fields. Includes FE for cell",
          notes.align = "l",
          omit=c("cell"), out=paste(od, "rw_baseline_fertility_qual.htm", sep="/"))

2016A Rwanda Soil Health Baseline - Farmer Perceived Fertility

	Ca	Mg	pH	Total.N	Total.C
	(1)	(2)	(3)	(4)	(5)
Farmer Opinion - Less Fertile	-112.045***	-19.157***	-0.121***	-0.0004	0.003
	(21.335)	(4.601)	(0.021)	(0.001)	(0.022)
Farmer Opinion - More Fertile	5.575	1.536	-0.002	-0.001	-0.003
	(23.554)	(5.079)	(0.023)	(0.001)	(0.024)
Constant	706.875*	84.054	4.808***	0.201***	3.302***
	(380.991)	(82.158)	(0.366)	(0.021)	(0.391)
Observations	2,443	2,443	2,443	2,443	2,443
R2	0.558	0.592	0.616	0.500	0.457
Adjusted R2	0.519	0.555	0.581	0.455	0.408
Residual Std. Error (df = 2240)	380.393	82.029	0.366	0.021	0.390
F Statistic (df = 202; 2240)	14.022***	16.105***	17.797***	11.085***	9.325***
Note:	p<0.1; p<0.05; p<0.01
	Reference category is same fertility as other fields. Includes FE for cell

Interpretation: Farmers understand their fields well. Their categorization of which field are more and less fertile corresponds to our quantified measures of soil health. The only features farmers don’t seem to get correct are nitrogen and carbon. The nitrogen and carbon levels are indistinguishable in ‘low fertility’ fields relative to the fields deemed to be the ‘same fertility.’ Reminder: We need to remember that farmers are only evaluting one of their fields thus we are not able to account for the quality of the farmer in assessing his/her fields.

Deeper dive into farmer perception of fertility

• Look at wet chem values for all soil features by farmer perception
• Run PCA on all soil attributes to see which principle components predict soil fertility
• Consider adding additional control variables into model (like Ca as control for pH perception model)

# merge wetChem in with d
names(wetChem)[2:21] <- paste("wet.", names(wetChem)[2:21], sep = "")
d <- left_join(d, wetChem, by="SSN")

## Warning in left_join_impl(x, y, by$x, by$y, suffix$x, suffix$y): joining
## factor and character vector, coercing into character vector

wetVars <- names(d)[grep("wet.", names(d))]
for(i in 1:length(wetVars)){
  print(
  ggplot(data=d, aes(x=as.factor(client), y=d[,wetVars[i]])) + 
    geom_boxplot() +
    labs(x="Tubura Farmer", y=wetVars[i], title = paste("RW baseline wet chem - ", wetVars[i], sep = ""))
  )
}

## Warning: Removed 2206 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2206 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

## Warning: Removed 2199 rows containing non-finite values (stat_boxplot).

list7 <- lapply(wetVars, function(x){
  mod <- lm(as.formula(paste("d[,x] ~", "+ fertility_qual + as.factor(cell)", sep="")), data=d)
  return(mod)
})

suppressWarnings(
stargazer(list7, type="html", 
          title = "2016A Rwanda Soil Health Baseline - Farmer Perceived Fertility (wet chem)",
          covariate.labels = c("Farmer Opinion - Less Fertile",
                               "Farmer Opinion - More Fertile"),
          dep.var.caption = "",
          dep.var.labels = "",
          column.labels = c(gsub("wet.","", wetVars)),
          notes = "Reference category is same fertility as other fields. Includes FE for cell",
          notes.align = "l",
          omit=c("cell"), out=paste(od, "rw_baseline_fertility_qual_wet.htm", sep="/"))
)

2016A Rwanda Soil Health Baseline - Farmer Perceived Fertility (wet chem)

	pH	EC..S.	P	K	Ca	Mg	S	Na	Fe	Mn	B	Cu	Zn	C.E.C	TN	C.N	Exch..Acidity	Acid.Saturation	Exch.Al	OC
	(1)	(2)	(3)	(4)	(5)	(6)	(7)	(8)	(9)	(10)	(11)	(12)	(13)	(14)	(15)	(16)	(17)	(18)	(19)	(20)
Farmer Opinion - Less Fertile	-0.227	1.930	-9.111	-44.922	-23.678	-22.846	2.274	-0.079	22.320	-29.748	-0.064	-0.317	-0.224	0.138	0.004	-0.277	0.343**	9.657**	0.268**	0.153
	(0.147)	(11.629)	(19.670)	(28.712)	(150.522)	(36.856)	(2.236)	(2.929)	(17.023)	(21.301)	(0.222)	(0.337)	(0.764)	(1.126)	(0.008)	(0.627)	(0.160)	(3.686)	(0.124)	(0.135)
Farmer Opinion - More Fertile	-0.109	-7.216	-16.525	-69.198**	-187.493	-57.688	2.223	-0.854	-12.790	-10.391	-0.069	-0.278	-1.040	-1.369	-0.016*	0.287	0.125	3.831	0.091	-0.192
	(0.174)	(13.775)	(23.740)	(34.653)	(181.669)	(44.482)	(2.699)	(3.535)	(20.546)	(25.708)	(0.268)	(0.407)	(0.922)	(1.359)	(0.010)	(0.757)	(0.193)	(4.449)	(0.150)	(0.163)
Constant	6.225***	127.000***	8.910	213.000***	1,745.000***	435.000***	15.700**	24.300***	61.450	194.000***	0.415	2.670***	4.415**	15.650***	0.195***	11.750***	0.140	1.100	0.023	2.335***
	(0.406)	(32.067)	(55.599)	(81.159)	(425.475)	(104.178)	(6.321)	(8.278)	(48.119)	(60.210)	(0.627)	(0.953)	(2.160)	(3.182)	(0.023)	(1.772)	(0.451)	(10.419)	(0.351)	(0.383)
Observations	237	237	244	244	244	244	244	244	244	244	244	244	244	244	244	244	244	244	244	244
R2	0.742	0.580	0.702	0.653	0.760	0.755	0.729	0.705	0.769	0.688	0.525	0.693	0.540	0.752	0.773	0.671	0.775	0.777	0.797	0.731
Adjusted R2	0.425	0.064	0.348	0.240	0.475	0.463	0.407	0.354	0.494	0.318	-0.039	0.329	-0.006	0.457	0.504	0.280	0.506	0.511	0.555	0.412
Residual Std. Error	0.574 (df = 106)	45.349 (df = 106)	78.629 (df = 111)	114.776 (df = 111)	601.713 (df = 111)	147.330 (df = 111)	8.940 (df = 111)	11.707 (df = 111)	68.051 (df = 111)	85.150 (df = 111)	0.887 (df = 111)	1.347 (df = 111)	3.055 (df = 111)	4.501 (df = 111)	0.033 (df = 111)	2.506 (df = 111)	0.638 (df = 111)	14.735 (df = 111)	0.496 (df = 111)	0.541 (df = 111)
F Statistic	2.344*** (df = 130; 106)	1.125 (df = 130; 106)	1.983*** (df = 132; 111)	1.580*** (df = 132; 111)	2.664*** (df = 132; 111)	2.586*** (df = 132; 111)	2.264*** (df = 132; 111)	2.010*** (df = 132; 111)	2.796*** (df = 132; 111)	1.857*** (df = 132; 111)	0.930 (df = 132; 111)	1.902*** (df = 132; 111)	0.988 (df = 132; 111)	2.551*** (df = 132; 111)	2.867*** (df = 132; 111)	1.715*** (df = 132; 111)	2.888*** (df = 132; 111)	2.923*** (df = 132; 111)	3.293*** (df = 132; 111)	2.290*** (df = 132; 111)
Note:	p<0.1; p<0.05; p<0.01
	Reference category is same fertility as other fields. Includes FE for cell

Interpretation: Our sample size decreases considerably when we look only at wet chemistry results. Thus, we do not see the same signficant relationships we saw between farmer perceived fertility and soil characteristics we saw when looking at the predicted values.

Principal Component Analysis (predicted values)

pca1 <- prcomp(d[,soilVars], scale=TRUE, center=TRUE)
print(pca1)

## Standard deviations:
## [1] 1.6054877 1.4130381 0.4829896 0.3401430 0.2770491
## 
## Rotation:
##                 PC1        PC2         PC3         PC4         PC5
## m3.Ca    0.59320505 -0.1382841  0.17987753 -0.19239465 -0.74807329
## m3.Mg    0.57530571 -0.0363033 -0.77066159  0.02943037  0.27003700
## pH       0.55976522  0.2080885  0.58530931  0.27208080  0.47617971
## Total.N  0.05235072 -0.6836420  0.17634506 -0.60421041  0.36568460
## Total.C -0.03245639 -0.6847572  0.00634184  0.72320119 -0.08363026

plot(pca1)

pca1$rotation

##                 PC1        PC2         PC3         PC4         PC5
## m3.Ca    0.59320505 -0.1382841  0.17987753 -0.19239465 -0.74807329
## m3.Mg    0.57530571 -0.0363033 -0.77066159  0.02943037  0.27003700
## pH       0.55976522  0.2080885  0.58530931  0.27208080  0.47617971
## Total.N  0.05235072 -0.6836420  0.17634506 -0.60421041  0.36568460
## Total.C -0.03245639 -0.6847572  0.00634184  0.72320119 -0.08363026

The first principal component is composed primarily of soil pH related variables, Ca, Mg, and pH. The second capture N and C. These groupings (pH grouping and C and N) are not all that surprising given that our predicted soil variable set is fairly limited.

ggplot(as.data.frame(pca1$x),aes(x=PC1,y=PC2, color=d$fertility_qual)) + geom_point() + 
  labs(title = "PCA of soil attributes and farmer perceived soil fertility",
       x = "First PCA", y= "Second PCA", color="Field Quality")

When we layer farmer perceived soil fertility on top of the principal component scatter plot, no clear pattern emergres.

Principal Component Analysis (wet chemistry values)

wetVal <- d[complete.cases(d[,wetVars]),]

pca2 <- prcomp(wetVal[,c("wet.C.E.C", "wet.pH", "wet.Mg", "wet.Ca")], center=TRUE, scale=TRUE)

plot(pca2)

ggplot(as.data.frame(pca2$x),aes(x=PC1,y=PC2)) + geom_point()

pca2$rotation

##                  PC1        PC2        PC3        PC4
## wet.C.E.C -0.5251751  0.3721436 -0.2834744  0.7108745
## wet.pH    -0.4454858 -0.8097501  0.3125642  0.2194329
## wet.Mg    -0.4972204  0.4418079  0.6689034 -0.3318824
## wet.Ca    -0.5277362 -0.1030520 -0.6119756 -0.5799661

# put pca2$x PC1 in the main data to run the fertility perception model.
#mod8 <- lm(

suppressWarnings(
stargazer(list7, type="html", 
          title = "2016A Rwanda Soil Health Baseline - Farmer Perceived Fertility (wet chem)",
          covariate.labels = c("Farmer Opinion - Less Fertile",
                               "Farmer Opinion - More Fertile"),
          dep.var.caption = "",
          dep.var.labels = "",
          column.labels = c(gsub("wet.","", wetVars)),
          notes = "Reference category is same fertility as other fields. Includes FE for cell",
          notes.align = "l",
          omit=c("cell"), out=paste(od, "rw_baseline_fertility_qual_wet.htm", sep="/"))
)

2016A Rwanda Soil Health Baseline - Farmer Perceived Fertility (wet chem)

	pH	EC..S.	P	K	Ca	Mg	S	Na	Fe	Mn	B	Cu	Zn	C.E.C	TN	C.N	Exch..Acidity	Acid.Saturation	Exch.Al	OC
	(1)	(2)	(3)	(4)	(5)	(6)	(7)	(8)	(9)	(10)	(11)	(12)	(13)	(14)	(15)	(16)	(17)	(18)	(19)	(20)
Farmer Opinion - Less Fertile	-0.227	1.930	-9.111	-44.922	-23.678	-22.846	2.274	-0.079	22.320	-29.748	-0.064	-0.317	-0.224	0.138	0.004	-0.277	0.343**	9.657**	0.268**	0.153
	(0.147)	(11.629)	(19.670)	(28.712)	(150.522)	(36.856)	(2.236)	(2.929)	(17.023)	(21.301)	(0.222)	(0.337)	(0.764)	(1.126)	(0.008)	(0.627)	(0.160)	(3.686)	(0.124)	(0.135)
Farmer Opinion - More Fertile	-0.109	-7.216	-16.525	-69.198**	-187.493	-57.688	2.223	-0.854	-12.790	-10.391	-0.069	-0.278	-1.040	-1.369	-0.016*	0.287	0.125	3.831	0.091	-0.192
	(0.174)	(13.775)	(23.740)	(34.653)	(181.669)	(44.482)	(2.699)	(3.535)	(20.546)	(25.708)	(0.268)	(0.407)	(0.922)	(1.359)	(0.010)	(0.757)	(0.193)	(4.449)	(0.150)	(0.163)
Constant	6.225***	127.000***	8.910	213.000***	1,745.000***	435.000***	15.700**	24.300***	61.450	194.000***	0.415	2.670***	4.415**	15.650***	0.195***	11.750***	0.140	1.100	0.023	2.335***
	(0.406)	(32.067)	(55.599)	(81.159)	(425.475)	(104.178)	(6.321)	(8.278)	(48.119)	(60.210)	(0.627)	(0.953)	(2.160)	(3.182)	(0.023)	(1.772)	(0.451)	(10.419)	(0.351)	(0.383)
Observations	237	237	244	244	244	244	244	244	244	244	244	244	244	244	244	244	244	244	244	244
R2	0.742	0.580	0.702	0.653	0.760	0.755	0.729	0.705	0.769	0.688	0.525	0.693	0.540	0.752	0.773	0.671	0.775	0.777	0.797	0.731
Adjusted R2	0.425	0.064	0.348	0.240	0.475	0.463	0.407	0.354	0.494	0.318	-0.039	0.329	-0.006	0.457	0.504	0.280	0.506	0.511	0.555	0.412
Residual Std. Error	0.574 (df = 106)	45.349 (df = 106)	78.629 (df = 111)	114.776 (df = 111)	601.713 (df = 111)	147.330 (df = 111)	8.940 (df = 111)	11.707 (df = 111)	68.051 (df = 111)	85.150 (df = 111)	0.887 (df = 111)	1.347 (df = 111)	3.055 (df = 111)	4.501 (df = 111)	0.033 (df = 111)	2.506 (df = 111)	0.638 (df = 111)	14.735 (df = 111)	0.496 (df = 111)	0.541 (df = 111)
F Statistic	2.344*** (df = 130; 106)	1.125 (df = 130; 106)	1.983*** (df = 132; 111)	1.580*** (df = 132; 111)	2.664*** (df = 132; 111)	2.586*** (df = 132; 111)	2.264*** (df = 132; 111)	2.010*** (df = 132; 111)	2.796*** (df = 132; 111)	1.857*** (df = 132; 111)	0.930 (df = 132; 111)	1.902*** (df = 132; 111)	0.988 (df = 132; 111)	2.551*** (df = 132; 111)	2.867*** (df = 132; 111)	1.715*** (df = 132; 111)	2.888*** (df = 132; 111)	2.923*** (df = 132; 111)	3.293*** (df = 132; 111)	2.290*** (df = 132; 111)
Note:	p<0.1; p<0.05; p<0.01
	Reference category is same fertility as other fields. Includes FE for cell

Measured Yields

We don’t have measured yield data for the Rwanda baseline. Skip this for now.

Distributions of soil health levels for different sub-groups

Visualizations

Soil health maps for soil health study areas

#crdref <- CRS('+proj=longlat +datum=WGS84')
crdref <- CRS('+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0')
e <- d[!is.na(d$lon),]
ss <- SpatialPointsDataFrame(coords = e[, c("lon", "lat")], data=e, proj4string = crdref)

rw <- getData("GADM", country='RW', level=3, path = "/Users/mlowes/drive/soil health study/data") # the higher the number, the higher the resolution

#ext.rw.ss matches points with spatial polygons in rw
ext.rw.ss <- extract(rw[, "NAME_3"], ss)
ss$spatialname <- ext.rw.ss$NAME_3

frw <- fortify(rw, region="NAME_3")
ss.soil <- aggregate(ss@data[,soilVars], by=list(ss@data$spatialname), function(x){
  mean(x, na.rm=T)
})

plotReady <- dplyr::left_join(frw, ss.soil, by=c("id"="Group.1"))

Plot simple summary of soil characteristics

Consider revising these maps to a smaller greographic unit. Add the name of the location for uninitiated users.

library(RColorBrewer)
mapList <- list()
for(i in 1:length(soilVars)){
mapRes <-  ggplot(plotReady, aes(x=long, y=lat, group=group)) + geom_path() + 
  geom_polygon(aes(fill=plotReady[,soilVars[i]])) + 
  scale_fill_gradientn(colours = rev(brewer.pal(9,"Reds")), # define colors
                       name = soilVars[i],
                       guide = guide_colorbar(legend.direction = "vertical")) + 
  theme_bw() + 
  labs(title=paste("Rwanda long term soil health baseline - 2016", soilVars[i], sep= " "), x = "Longitude", y="Latitude")
mapList[[i]] <- mapRes
print(mapRes)
} 

# This is a small experiment to combine raster (spdf) and leaflet and be able to access the data in the raster interactively.
#mapLayer <- sp::merge(rw, ss.soil, by.x="NAME_3", by.y="Group.1")

# fill = T, fillOpacity = 0.7, fillColor = d.fill, 
#         stroke = T, color = "white", weight = 2, dashArray = 3, 
#         opacity = 0.5, popup = county.tt(d)

# leaflet(mapLayer) %>% addTiles() %>%
#   setView(lng=rwanda$longitude, lat=rwanda$latitude, zoom=8) %>%
#   addPolygons(
#     stroke = TRUE, opacity=0.2, smoothFactor = 0.5, 
#     fillColor=mapLayer$pH, fillOpacity = 0.5)

pdf(file=paste(md, "rw_shs_baseline_soil_maps.pdf", sep = "/"), width=11, height=8.5)
for(i in 1:length(mapList)){
print(mapList[[i]])
}  
dev.off()

Interpolations of soil health values

Interpolate soil health values for full operating area using soil health study values. We want to eventually add all Rwandan soil values into a single dataset to update and hone these values. See here for more guidanace

note:

• Layer on the Tubura sites to the interpolated map.
• Use leaflet so you can zoom in and out more easily.
• Make it a raster layer that you can click on understand the values at different locations and the name of the location. I’ll need to make this a shiny app to have that functionality

The code below will run 5 K-fold cross validation to compare interpolation models. The output will be fed into the interpolate leaflet code below.

Check that I’m handling the projection correctly with Robert

#proj4string(ss) <- CRS("+init=epsg:4326")
ss <- spTransform(ss, CRS=("+proj=utm +zone=36N +datum=WGS84"))

# root mean sq error for evaluating models
RMSE <- function(observed, predicted) {
  sqrt(mean((predicted - observed)^2, na.rm=TRUE))
}

# set k folds to 5
set.seed(20161030)
nfolds <- 5
k <- kfold(ss, nfolds) # from dismo

# cross validation of models
ensrmse <- tpsrmse <- idwrmse <- rep(NA, 5) # assing multiple objects at once

cv <- function(x) {
  
  for(i in 1:nfolds) {
    train <- ss[k!=i,]
    test <- ss[k==i,]

  train <- train[!is.na(train@data[,x]),]
  
  # inverse distance weights
  m <- gstat(formula=as.formula(paste(x, '~ 1')), locations=train)
  p1 <- predict(m, newdata=test, debug.level=0)$var1.pred
  idwrmse[i] <-  RMSE(test@data[,x], p1) #idw rsme
  
  # krieging
  # m <- autoKrige(formula=as.formula(paste(x, "~ 1")), input_data = train)
  # p2 <- predict(m, newdata=test, debug.level=0)$var1.pred
  # krigrmse[i] <-  RMSE(test$OZDLYAV, p2)
  
  # thin plate spline
  m <- Tps(coordinates(train), train@data[,x]) 
  p3 <- predict(m, coordinates(test))
  tpsrmse[i] <-  RMSE(test@data[,x], p3)
  
  w <- c(idwrmse[i], tpsrmse[i]) # combine the rmse
  weights <- w / sum(w) # weight them
  ensemble <- p1 * weights[1] + p3 * weights[2] 
  # multiply predictions by weights
  ensrmse[i] <-  RMSE(test@data[,x], ensemble) # truly an ensemble result?
  }
  
  output <- rbind(idwrmse, tpsrmse, ensrmse)
  return(output)
  
}

Now loop over the variables of interest where x is the soilVar variable.

output <- lapply(soilVars, function(x){
  ini <- data.frame(cv(x))
  ini$ave <- apply(ini[,1:5], 1, function(y){mean(y, na.rm=T)})
  res <- paste("Best model is ", row.names(ini[which.min(ini$ave),]),  sep = "")
  return(list(ini, res))
})

Interpolated soil maps

r <- raster(res=1/12)
r <- crop(r, floor(extent(rw)))

maps <- lapply(soilVars, function(x){
  m <- Tps(coordinates(ss), ss@data[,x])
  # make raster layer with model, raster is rwanda empty raster, model is m
  tps <- interpolate(r, m)
  tps <- crop(tps, rw)
  tps <- mask(tps, rw) # cuts the tps raster down to the rw boundaries
  x <- gsub("m3.", "", x)
  
  pal <- colorNumeric(palette = "Reds", values(tps), na.color = "transparent")
  
  suppressWarnings(
  leaflet() %>% addTiles() %>%
  addRasterImage(tps, colors=pal, opacity = 0.8) %>%
  setView(lng=rwanda$longitude, lat=rwanda$latitude, zoom=8) %>%
  addLegend(pal = pal, values = values(tps), title = paste("Soil Value ", x, sep=""))
  )
})

save(maps,ss, file=paste(dd, "rw_baseline_interpolation_maps.Rdata", sep = "/"))

tagList(maps)

Print out the interpolated values for inclusion in the report.

Geographic Descriptors

This section will look at improving understanding of local context to inform local adaptation. It will also construct soil profiles to simplify the scaling of promising products and practices to targeted locations.

Propensity Score Matching

We need to do a more rigorous job of accounting for differences between Tubura farmers and identified control farmers. Execute propensity score matching (PSM) to identify control farmers that overlap with Tubura farmers with regard to their likelihood of being a Tubura farmer.

cor(d[, grep("betail_", names(d))], use='complete.obs')

##                        betail_ownedn_inka betail_ownedn_ihene
## betail_ownedn_inka             1.00000000         0.036402152
## betail_ownedn_ihene            0.03640215         1.000000000
## betail_ownedn_inkoko           0.09740274         0.127424693
## betail_ownedn_ingurube         0.02166420        -0.009667001
## betail_ownedn_intama           0.04245052         0.002625236
##                        betail_ownedn_inkoko betail_ownedn_ingurube
## betail_ownedn_inka               0.09740274            0.021664199
## betail_ownedn_ihene              0.12742469           -0.009667001
## betail_ownedn_inkoko             1.00000000            0.049416370
## betail_ownedn_ingurube           0.04941637            1.000000000
## betail_ownedn_intama             0.03041599            0.025487680
##                        betail_ownedn_intama
## betail_ownedn_inka              0.042450521
## betail_ownedn_ihene             0.002625236
## betail_ownedn_inkoko            0.030415986
## betail_ownedn_ingurube          0.025487680
## betail_ownedn_intama            1.000000000

names(d)[grep("betail_", names(d))] <- c("cows", "goats", "chickens", "pigs", "sheep")

psmVars <- paste(c("female", "age", "hhsize", "total.seasons",
                   "cows", "goats", "chickens", "pigs", "sheep"),
                   collapse=" + ")

reg <- glm(as.formula(paste("client ~", psmVars, sep="")), 
           family= binomial(link="logit"), data=d)
summary(reg)    

## 
## Call:
## glm(formula = as.formula(paste("client ~", psmVars, sep = "")), 
##     family = binomial(link = "logit"), data = d)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -3.5522  -0.8456   0.0376   0.9250   2.0863  
## 
## Coefficients:
##                Estimate Std. Error z value Pr(>|z|)    
## (Intercept)    0.408940   0.203191   2.013   0.0442 *  
## female        -0.749686   0.097393  -7.698 1.39e-14 ***
## age           -0.024394   0.003378  -7.221 5.16e-13 ***
## hhsize         0.037275   0.022980   1.622   0.1048    
## total.seasons  0.530099   0.028803  18.404  < 2e-16 ***
## cows           0.007891   0.017934   0.440   0.6599    
## goats         -0.004426   0.030020  -0.147   0.8828    
## chickens       0.023011   0.017794   1.293   0.1959    
## pigs           0.052035   0.057838   0.900   0.3683    
## sheep          0.053211   0.070949   0.750   0.4533    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 3386.7  on 2442  degrees of freedom
## Residual deviance: 2566.6  on 2433  degrees of freedom
## AIC: 2586.6
## 
## Number of Fisher Scoring iterations: 5

# summarize predicted probabilities
pr <- data.frame(pr_score = predict(reg, type='response'), treat = d$client)

# graph
psmGraph <- ggplot() + geom_histogram(data=subset(pr, pr$treat==1), aes(x = pr_score, y=..count.., fill=as.factor(treat)), bins=80, position = "identity") +
    geom_histogram(data=subset(pr, pr$treat==0), aes(x=pr_score, y=-..count.., fill=as.factor(treat)), bins=80, position = "identity") +
    scale_y_continuous(limits=c(-150,150)) + 
  labs(title ="PSM score overlap", x = "PSM score", y="Farmer count",
       fill="Tubura/Control")

print(psmGraph)

pdf(file=paste(od, "rw_baseline_psm_overlap.pdf", sep="/"), height=8.5, width=11)
print(psmGraph)
dev.off()

## quartz_off_screen 
##                 2

Interpretation We have some overlap but it’s clear that Tubura farmers occupy a different range than the identified control farmers. Let’s continue with the PSM matching process but restrict ourselves to Tubura and control farmers that meet a certain PSM matching radius.

Notes on PSM process:

We have to indicate a variable for matching. I’m choosing pH as we know it to be an issue in most of our operating areas and addressing soil acidity has numerous residual benefits to soil health. I’ll want to do this for all soil outcomes, however.

• As a next step, I’d like to identify the matched subset and then regress Tubura tenure on soil outcomes. Does that make sense?
• I chose a caliper of 0.25. I should review this process with Maya to make certain I’m following best practice. I sort of just pulled that sd figure out of the sky.
• An initial check of the match quality using a common model indicates that the matches are poor.

# PSM prep
tr <- cbind(d$client)
x <- d[, unlist(strsplit(psmVars, " + ", fixed=T))]
y <- c("m3.Ca", "m3.Mg", "pH", "Total.N", "Total.C")


# PSM
set.seed(20161102)
m <- lapply(y, function(response){

  suppressWarnings(
  mod <- Match(Y = d[,response], Tr = tr, X = reg$fitted, ties=FALSE, replace=FALSE, caliper=0.25, estimand = "ATE")    
  )
  matchRes <- MatchBalance(tr ~ d[,response], match.out=mod, nboots=500, data=d, print.level = 0)
  return(list(mod, matchRes))
})
#lapply(m, summary)

Now check the naive model approach for PSM balance.

matchRes <- do.call(rbind, lapply(1:length(m), function(model){
  val <- as.data.frame(cbind(
    standard.diff=m[[model]][[2]]$AfterMatching[[1]]$sdiff, 
    var.ratio = m[[model]][[2]]$AfterMatching[[1]]$var.ratio,
    sdiff.adj = m[[model]][[2]]$AfterMatching[[1]]$sdiff/100))
  return(val)
}))
rownames(matchRes) <- y

print(kable(matchRes))

	standard.diff	var.ratio	sdiff.adj
m3.Ca	-1.678540	0.8498607	-0.0167854
m3.Mg	-12.306011	0.7311426	-0.1230601
pH	6.233730	1.0749892	0.0623373
Total.N	-1.873108	0.9551298	-0.0187311
Total.C	-2.495694	1.0376312	-0.0249569

Interpretation: We want to see standard mean differences less than the absolute value of 0.25 (or 0.1 if we’re being conservative) and variance ratios close to 1 but certainly between 0.5 and 2.

According to the CRAN summary, sdiff is the standardized difference between the treatment and control units multiplied by 100. If I divide by 100, the values come much closer to reasonable value.

Let the PSM models vary

The common model approach doesn’t seem to be working for any of the variables. I’m going to rework the modeling approach so we can fit different models for each outcome upon which we’re trying to match.

d$age2 <- d$age^2
d$hhsize_age <- d$hhsize*d$age
d$hhsize2 <- d$hhsize^2

psmList <- list(
  list(tr = d$client,
       psmVars = paste(c("female", "age", "hhsize", "as.factor(district)",
                         "cows", "goats", "chickens", "pigs", "sheep"),
                   collapse=" + "),
       y="m3.Ca"),
  list(tr = d$client,
       psmVars = paste(c("female", "age", "hhsize", "as.factor(district)",
                   "cows", "goats", "chickens", "pigs", "sheep"),
                   collapse=" + "),
       y="m3.Mg"),
  list(tr = d$client,
       psmVars = paste(c("female", "age", "hhsize", "as.factor(district)",
                   "cows", "goats", "chickens", "pigs", "sheep"),
                   collapse=" + "),
       y="pH"),
  list(tr = d$client,
       psmVars = paste(c("female", "age", "hhsize", "as.factor(district)",
                   "cows", "goats", "chickens", "pigs", "sheep"),
                   collapse=" + "),
       y="Total.N"),
  list(tr = d$client,
       psmVars = paste(c("female", "age", "hhsize","as.factor(district)",
                   "cows", "goats", "chickens", "pigs", "sheep"),
                   collapse=" + "),
       y="Total.C")
)

# PSM
set.seed(20161102)
m <- lapply(psmList, function(listInput){

  # run glm regression:
  reg <- glm(as.formula(paste("client ~", listInput$psmVars, sep="")),  family= binomial(link="logit"), data=d)
  
  suppressWarnings(
  mod <- Match(Y = d[,listInput$y], Tr = listInput$tr, X = reg$fitted, ties=FALSE, replace=FALSE, caliper=0.25, estimand = "ATE")   
  )
  matchRes <- MatchBalance(tr ~ d[,listInput$y], match.out=mod, nboots=500, data=d, print.level = 0)
  return(list(mod, matchRes))
})
#lapply(m, summary)

The models can now vary by outcome. Let’s see if we can improve our results.

matchRes <- do.call(rbind, lapply(1:length(m), function(model){
  val <- as.data.frame(cbind(
    standard.diff=m[[model]][[2]]$AfterMatching[[1]]$sdiff, 
    var.ratio = m[[model]][[2]]$AfterMatching[[1]]$var.ratio,
    sdiff.adj = m[[model]][[2]]$AfterMatching[[1]]$sdiff/100))
  return(val)
}))
rownames(matchRes) <- y

print(kable(matchRes))

	standard.diff	var.ratio	sdiff.adj
m3.Ca	-4.128730	0.8694964	-0.0412873
m3.Mg	-5.359542	0.9072695	-0.0535954
pH	-2.668648	0.9911040	-0.0266865
Total.N	-5.507115	1.0038824	-0.0550712
Total.C	-2.885680	1.0129954	-0.0288568

Interpretation If undivide the standardized mean differences by 100, we meet the balance criteria of the standardized mean difference being close to 0 and the variance being close to 1. Let’s print out the model results to see how Tubura and control farmers compare on key soil meterics. These results should supercede the naive balance tables presented above.

coefTable <- do.call(rbind, lapply(1:length(m), function(model){
  beta = round(m[[model]][[1]]$est.noadj,3)
  pval = (1 - pnorm(abs(m[[model]][[1]]$est/m[[model]][[1]]$se.standard))) * 2
  pval = ifelse(pval < 0.001, "0.001", round(pval, 3))
  
  res = data.frame(beta, pval)
  return(res)
}))
row.names(coefTable) <- y
coefTable$pval.adj <- round(p.adjust(coefTable$pval, method="fdr"),3)

print(kable(coefTable))

	beta	pval	pval.adj
m3.Ca	-21.691	0.218	0.363
m3.Mg	-6.574	0.108	0.270
pH	-0.015	0.402	0.402
Total.N	-0.002	0.091	0.270
Total.C	-0.015	0.368	0.402

Interpretation: Propensity score matching gives us a comparable treatment and control group. The table above shows that after matching on those characteristics, there are effectively no differences between One Acre Fund farmer and Tubura farmers. The unadjusted p-values show 1AF farmers to have slow levels of soil nitrogen but this finding disappears if we account for running multiple matching models.

Models with PSM matched farmers

–end